HEADER PROTEIN TRANSPORT 16-NOV-06 2J9W TITLE STRUCTURAL INSIGHT INTO THE ESCRT-I-II LINK AND ITS ROLE IN MVB TITLE 2 TRAFFICKING COMPND MOL_ID: 1; COMPND 2 MOLECULE: VPS28-PROV PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 123-221; COMPND 5 SYNONYM: VPS28; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 3 ORGANISM_COMMON: AFRICAN CLAWED FROG; SOURCE 4 ORGANISM_TAXID: 8355; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: C41; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: POPTH KEYWDS NZF FINGER, HIV BUDDING, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR D.J.GILL,H.L.TEO,J.SUN,O.PERISIC,D.B.VEPRINTSEV,S.D.EMR,R.L.WILLIAMS REVDAT 5 01-MAY-24 2J9W 1 REMARK REVDAT 4 24-JAN-18 2J9W 1 SOURCE REVDAT 3 13-JUL-11 2J9W 1 VERSN REVDAT 2 24-FEB-09 2J9W 1 VERSN REVDAT 1 23-JAN-07 2J9W 0 JRNL AUTH D.J.GILL,H.TEO,J.SUN,O.PERISIC,D.B.VEPRINTSEV,S.D.EMR, JRNL AUTH 2 R.L.WILLIAMS JRNL TITL STRUCTURAL INSIGHT INTO THE ESCRT-I/-II LINK AND ITS ROLE IN JRNL TITL 2 MVB TRAFFICKING. JRNL REF EMBO J. V. 26 600 2007 JRNL REFN ISSN 0261-4189 JRNL PMID 17215868 JRNL DOI 10.1038/SJ.EMBOJ.7601501 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 88.2 REMARK 3 NUMBER OF REFLECTIONS : 37809 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2027 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1273 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2880 REMARK 3 BIN FREE R VALUE SET COUNT : 90 REMARK 3 BIN FREE R VALUE : 0.2880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1638 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 134 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.62000 REMARK 3 B22 (A**2) : -0.35000 REMARK 3 B33 (A**2) : -0.30000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.14000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.067 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.068 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.043 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.987 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1679 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2261 ; 1.502 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 204 ; 4.421 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 90 ;28.520 ;24.222 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 327 ;14.919 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;18.990 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 250 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1266 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 823 ; 0.232 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1176 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 99 ; 0.165 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 65 ; 0.233 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 19 ; 0.268 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1036 ; 1.162 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1633 ; 1.773 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 707 ; 3.004 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 625 ; 4.382 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 7 A 11 REMARK 3 ORIGIN FOR THE GROUP (A): 17.6486 8.6340 28.5673 REMARK 3 T TENSOR REMARK 3 T11: .1095 T22: .1222 REMARK 3 T33: .1018 T12: -.0069 REMARK 3 T13: -.0012 T23: -.0111 REMARK 3 L TENSOR REMARK 3 L11: 2.5147 L22: 16.6869 REMARK 3 L33: 1.4365 L12: -6.4066 REMARK 3 L13: .5915 L23: -.8188 REMARK 3 S TENSOR REMARK 3 S11: .0448 S12: .0602 S13: -.1291 REMARK 3 S21: -.1173 S22: -.0486 S23: -.3375 REMARK 3 S31: .0746 S32: .1373 S33: .0037 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 12 A 30 REMARK 3 ORIGIN FOR THE GROUP (A): 12.9779 20.4084 40.9041 REMARK 3 T TENSOR REMARK 3 T11: .0428 T22: .0410 REMARK 3 T33: .0576 T12: .0026 REMARK 3 T13: -.0033 T23: .0101 REMARK 3 L TENSOR REMARK 3 L11: .9692 L22: 3.0552 REMARK 3 L33: 5.7403 L12: .2173 REMARK 3 L13: -.1035 L23: 2.8273 REMARK 3 S TENSOR REMARK 3 S11: -.0152 S12: .0074 S13: -.0156 REMARK 3 S21: .0427 S22: .0619 S23: -.0891 REMARK 3 S31: .1365 S32: .1335 S33: -.0467 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 31 A 37 REMARK 3 ORIGIN FOR THE GROUP (A): 15.0394 29.6413 54.3778 REMARK 3 T TENSOR REMARK 3 T11: .0797 T22: .0792 REMARK 3 T33: .0695 T12: .0144 REMARK 3 T13: -.0060 T23: -.0048 REMARK 3 L TENSOR REMARK 3 L11: 5.8869 L22: 5.8600 REMARK 3 L33: 1.6768 L12: 3.8606 REMARK 3 L13: -1.5563 L23: -1.1661 REMARK 3 S TENSOR REMARK 3 S11: .0110 S12: -.1982 S13: .0142 REMARK 3 S21: .2317 S22: -.0204 S23: .2184 REMARK 3 S31: .1111 S32: -.1708 S33: .0095 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 38 A 52 REMARK 3 ORIGIN FOR THE GROUP (A): 18.9580 28.1281 40.0465 REMARK 3 T TENSOR REMARK 3 T11: .0428 T22: .0411 REMARK 3 T33: .0685 T12: .0102 REMARK 3 T13: .0069 T23: .0034 REMARK 3 L TENSOR REMARK 3 L11: 2.6359 L22: 2.4859 REMARK 3 L33: 5.3761 L12: 1.3988 REMARK 3 L13: 1.9054 L23: 3.0443 REMARK 3 S TENSOR REMARK 3 S11: -.0104 S12: .0312 S13: .0009 REMARK 3 S21: -.0136 S22: .0312 S23: -.0589 REMARK 3 S31: -.0030 S32: .1041 S33: -.0209 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 53 A 60 REMARK 3 ORIGIN FOR THE GROUP (A): 10.9680 25.4587 26.9714 REMARK 3 T TENSOR REMARK 3 T11: .1144 T22: .1160 REMARK 3 T33: .0920 T12: -.0102 REMARK 3 T13: .0036 T23: -.0048 REMARK 3 L TENSOR REMARK 3 L11: 1.5362 L22: 3.8258 REMARK 3 L33: 1.6841 L12: -.5973 REMARK 3 L13: -1.3673 L23: .7492 REMARK 3 S TENSOR REMARK 3 S11: .0083 S12: .1234 S13: .1365 REMARK 3 S21: -.1806 S22: -.0394 S23: .1371 REMARK 3 S31: -.1551 S32: -.1357 S33: .0311 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 61 A 66 REMARK 3 ORIGIN FOR THE GROUP (A): 7.2442 31.7621 34.2682 REMARK 3 T TENSOR REMARK 3 T11: .0674 T22: .0608 REMARK 3 T33: .0745 T12: .0018 REMARK 3 T13: -.0004 T23: .0116 REMARK 3 L TENSOR REMARK 3 L11: 4.9960 L22: 6.3510 REMARK 3 L33: 6.5400 L12: 3.6491 REMARK 3 L13: 4.3179 L23: -.0633 REMARK 3 S TENSOR REMARK 3 S11: -.0055 S12: .0658 S13: .1744 REMARK 3 S21: -.0781 S22: -.0572 S23: .3626 REMARK 3 S31: -.1738 S32: -.3433 S33: .0627 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 67 A 81 REMARK 3 ORIGIN FOR THE GROUP (A): 17.6114 38.1761 43.8888 REMARK 3 T TENSOR REMARK 3 T11: .0626 T22: .0545 REMARK 3 T33: .0681 T12: .0007 REMARK 3 T13: .0034 T23: -.0020 REMARK 3 L TENSOR REMARK 3 L11: 1.8155 L22: .1585 REMARK 3 L33: 1.9158 L12: .4751 REMARK 3 L13: 1.6771 L23: .5508 REMARK 3 S TENSOR REMARK 3 S11: -.0642 S12: .0342 S13: .1879 REMARK 3 S21: .0140 S22: .0121 S23: -.1012 REMARK 3 S31: -.1626 S32: .1996 S33: .0520 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 82 A 94 REMARK 3 ORIGIN FOR THE GROUP (A): 8.7333 35.4861 50.7560 REMARK 3 T TENSOR REMARK 3 T11: .0480 T22: .0411 REMARK 3 T33: .0483 T12: .0090 REMARK 3 T13: .0071 T23: .0000 REMARK 3 L TENSOR REMARK 3 L11: 3.8949 L22: 3.2078 REMARK 3 L33: 3.1288 L12: 1.7024 REMARK 3 L13: 1.4360 L23: 1.3480 REMARK 3 S TENSOR REMARK 3 S11: -.0145 S12: -.1514 S13: .0941 REMARK 3 S21: .0813 S22: -.0049 S23: .0333 REMARK 3 S31: -.0894 S32: -.0559 S33: .0195 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 95 A 108 REMARK 3 ORIGIN FOR THE GROUP (A): 2.9009 23.3846 36.5820 REMARK 3 T TENSOR REMARK 3 T11: .0323 T22: .0450 REMARK 3 T33: .0689 T12: .0097 REMARK 3 T13: .0059 T23: .0122 REMARK 3 L TENSOR REMARK 3 L11: 3.8371 L22: 5.6564 REMARK 3 L33: 7.4002 L12: .4676 REMARK 3 L13: .6169 L23: 2.5504 REMARK 3 S TENSOR REMARK 3 S11: .0118 S12: .1415 S13: -.1867 REMARK 3 S21: -.1310 S22: -.1007 S23: .2806 REMARK 3 S31: .2369 S32: -.3376 S33: .0889 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.00 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2J9W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-NOV-06. REMARK 100 THE DEPOSITION ID IS D_1290030502. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-06 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : KHOZU REMARK 200 OPTICS : TORODIAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8573 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 44.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.3 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 45.7 REMARK 200 DATA REDUNDANCY IN SHELL : 1.17 REMARK 200 R MERGE FOR SHELL (I) : 0.33000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.280 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: SE DATASET FROM SEMET SUBSTITUTED CRYSTAL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15-25% PEG 600, 0.15M POTASSIUM REMARK 280 THIOCYANATE, 0.2M SODIUM CHLORIDE, 0.1M GUANIDINE HYDROCHLORIDE, REMARK 280 0.1M SODIUM CACODYLATE PH 6.5, PH 6.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 44.85650 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 221 REMARK 465 HIS B 120 REMARK 465 HIS B 121 REMARK 465 SER B 221 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 CG MET B 161 O HOH B 2027 2.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2041 O HOH B 2027 2657 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG B 148 -7.76 -140.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2J9U RELATED DB: PDB REMARK 900 2 ANGSTROM X-RAY STRUCTURE OF THE YEAST ESCRT-I VPS28 C-TERMINUS IN REMARK 900 COMPLEX WITH THE NZF-N DOMAIN FROM ESCRT-II REMARK 900 RELATED ID: 2J9V RELATED DB: PDB REMARK 900 2 ANGSTROM X-RAY STRUCTURE OF THE YEAST ESCRT-I VPS28 C-TERMINUS DBREF 2J9W A 123 221 UNP Q7T0W4 Q7T0W4_XENLA 123 221 DBREF 2J9W B 123 221 UNP Q7T0W4 Q7T0W4_XENLA 123 221 SEQADV 2J9W HIS A 120 UNP Q7T0W4 EXPRESSION TAG SEQADV 2J9W HIS A 121 UNP Q7T0W4 EXPRESSION TAG SEQADV 2J9W MET A 122 UNP Q7T0W4 EXPRESSION TAG SEQADV 2J9W HIS B 120 UNP Q7T0W4 EXPRESSION TAG SEQADV 2J9W HIS B 121 UNP Q7T0W4 EXPRESSION TAG SEQADV 2J9W MET B 122 UNP Q7T0W4 EXPRESSION TAG SEQRES 1 A 102 HIS HIS MET GLY ASN LEU ASN ARG CYS ILE ALA ASP ILE SEQRES 2 A 102 VAL SER LEU PHE ILE THR VAL MET ASP LYS LEU ARG LEU SEQRES 3 A 102 GLU ILE ARG ALA MET ASP GLU ILE GLN PRO ASP LEU ARG SEQRES 4 A 102 GLU LEU MET GLU THR MET ASN ARG MET SER HIS LEU PRO SEQRES 5 A 102 PRO ASP PHE GLU GLY ARG GLU LYS VAL SER GLN TRP LEU SEQRES 6 A 102 GLN LYS LEU SER SER MET SER ALA SER ASP GLU LEU ASP SEQRES 7 A 102 ASP SER GLN VAL ARG GLN MET LEU PHE ASP LEU GLU SER SEQRES 8 A 102 ALA TYR ASN ALA PHE ASN ARG PHE LEU HIS SER SEQRES 1 B 102 HIS HIS MET GLY ASN LEU ASN ARG CYS ILE ALA ASP ILE SEQRES 2 B 102 VAL SER LEU PHE ILE THR VAL MET ASP LYS LEU ARG LEU SEQRES 3 B 102 GLU ILE ARG ALA MET ASP GLU ILE GLN PRO ASP LEU ARG SEQRES 4 B 102 GLU LEU MET GLU THR MET ASN ARG MET SER HIS LEU PRO SEQRES 5 B 102 PRO ASP PHE GLU GLY ARG GLU LYS VAL SER GLN TRP LEU SEQRES 6 B 102 GLN LYS LEU SER SER MET SER ALA SER ASP GLU LEU ASP SEQRES 7 B 102 ASP SER GLN VAL ARG GLN MET LEU PHE ASP LEU GLU SER SEQRES 8 B 102 ALA TYR ASN ALA PHE ASN ARG PHE LEU HIS SER FORMUL 3 HOH *134(H2 O) HELIX 1 1 GLY A 123 LEU A 145 1 23 HELIX 2 2 ALA A 149 MET A 167 1 19 HELIX 3 3 PHE A 174 SER A 189 1 16 HELIX 4 4 ASP A 197 HIS A 220 1 24 HELIX 5 5 GLY B 123 LEU B 145 1 23 HELIX 6 6 ALA B 149 MET B 167 1 19 HELIX 7 7 GLY B 176 SER B 189 1 14 HELIX 8 8 ASP B 197 HIS B 220 1 24 CRYST1 25.997 89.713 40.384 90.00 95.13 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.038466 0.000000 0.003453 0.00000 SCALE2 0.000000 0.011147 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024862 0.00000 MTRIX1 1 -0.999673 0.025394 -0.002661 19.76140 1 MTRIX2 1 -0.022532 -0.828357 0.559745 6.43530 1 MTRIX3 1 0.012009 0.559623 0.828660 -2.08930 1 TER 838 HIS A 220 TER 1652 HIS B 220 HETATM 1653 O HOH A2001 17.327 0.299 26.551 1.00 29.79 O HETATM 1654 O HOH A2002 20.991 -0.367 26.295 1.00 31.76 O HETATM 1655 O HOH A2003 15.205 4.139 27.761 1.00 30.37 O HETATM 1656 O HOH A2004 22.305 6.989 27.826 1.00 44.62 O HETATM 1657 O HOH A2005 20.183 6.782 31.420 1.00 35.81 O HETATM 1658 O HOH A2006 17.386 13.608 24.241 1.00 31.34 O HETATM 1659 O HOH A2007 18.786 18.570 33.311 1.00 33.38 O HETATM 1660 O HOH A2008 17.117 15.551 39.676 1.00 32.35 O HETATM 1661 O HOH A2009 15.473 21.086 50.295 1.00 27.83 O HETATM 1662 O HOH A2010 8.125 20.344 53.517 1.00 34.69 O HETATM 1663 O HOH A2011 13.745 18.952 49.706 1.00 32.35 O HETATM 1664 O HOH A2012 22.655 25.341 47.612 1.00 39.11 O HETATM 1665 O HOH A2013 12.939 30.854 54.969 1.00 17.66 O HETATM 1666 O HOH A2014 9.275 29.771 56.151 1.00 37.34 O HETATM 1667 O HOH A2015 4.841 26.223 53.246 1.00 42.14 O HETATM 1668 O HOH A2016 4.566 26.486 50.817 1.00 34.37 O HETATM 1669 O HOH A2017 19.750 31.256 56.078 1.00 21.75 O HETATM 1670 O HOH A2018 9.167 33.306 57.191 1.00 39.15 O HETATM 1671 O HOH A2019 26.001 30.462 53.315 1.00 32.30 O HETATM 1672 O HOH A2020 29.128 31.755 50.567 1.00 15.30 O HETATM 1673 O HOH A2021 21.279 25.778 50.441 1.00 26.94 O HETATM 1674 O HOH A2022 24.823 30.630 41.655 1.00 22.96 O HETATM 1675 O HOH A2023 21.544 23.095 42.847 1.00 37.79 O HETATM 1676 O HOH A2024 20.787 26.911 46.772 1.00 16.14 O HETATM 1677 O HOH A2025 24.151 32.471 39.367 1.00 21.47 O HETATM 1678 O HOH A2026 23.840 27.382 40.684 1.00 17.38 O HETATM 1679 O HOH A2027 25.029 22.086 38.278 1.00 19.95 O HETATM 1680 O HOH A2028 17.593 15.586 22.710 1.00 35.05 O HETATM 1681 O HOH A2029 19.383 20.303 36.351 1.00 25.05 O HETATM 1682 O HOH A2030 20.878 23.468 35.667 1.00 27.03 O HETATM 1683 O HOH A2031 22.593 25.042 31.189 1.00 27.85 O HETATM 1684 O HOH A2032 13.451 26.486 27.218 1.00 26.97 O HETATM 1685 O HOH A2033 30.266 30.723 53.311 1.00 30.19 O HETATM 1686 O HOH A2034 9.745 32.425 30.090 1.00 25.29 O HETATM 1687 O HOH A2035 2.750 30.417 30.496 1.00 28.60 O HETATM 1688 O HOH A2036 3.130 30.967 37.444 1.00 24.30 O HETATM 1689 O HOH A2037 10.373 35.102 30.921 1.00 36.71 O HETATM 1690 O HOH A2038 8.257 36.069 40.833 1.00 28.36 O HETATM 1691 O HOH A2039 17.341 35.925 34.810 1.00 41.05 O HETATM 1692 O HOH A2040 20.702 35.917 40.985 1.00 15.27 O HETATM 1693 O HOH A2041 17.451 42.568 36.778 1.00 23.84 O HETATM 1694 O HOH A2042 6.294 31.770 54.744 1.00 30.93 O HETATM 1695 O HOH A2043 3.515 39.291 42.519 1.00 27.54 O HETATM 1696 O HOH A2044 22.584 36.546 43.148 1.00 22.27 O HETATM 1697 O HOH A2045 28.180 42.780 47.862 1.00 27.24 O HETATM 1698 O HOH A2046 23.623 44.348 50.706 1.00 20.96 O HETATM 1699 O HOH A2047 23.878 40.994 55.162 1.00 26.69 O HETATM 1700 O HOH A2048 19.714 43.274 50.138 1.00 31.61 O HETATM 1701 O HOH A2049 15.874 41.354 52.775 1.00 34.50 O HETATM 1702 O HOH A2050 20.192 40.527 55.776 1.00 26.38 O HETATM 1703 O HOH A2051 18.650 40.219 57.921 1.00 28.34 O HETATM 1704 O HOH A2052 9.142 41.407 56.696 1.00 20.55 O HETATM 1705 O HOH A2053 6.352 38.627 60.067 1.00 35.50 O HETATM 1706 O HOH A2054 11.610 39.127 58.759 1.00 26.09 O HETATM 1707 O HOH A2055 7.131 34.036 55.947 1.00 17.66 O HETATM 1708 O HOH A2056 4.207 38.247 51.756 1.00 24.02 O HETATM 1709 O HOH A2057 7.640 41.228 49.917 1.00 24.95 O HETATM 1710 O HOH A2058 3.222 36.654 56.647 1.00 37.95 O HETATM 1711 O HOH A2059 1.350 38.123 44.555 1.00 31.14 O HETATM 1712 O HOH A2060 1.637 39.744 47.349 1.00 29.75 O HETATM 1713 O HOH A2061 4.107 27.527 48.644 1.00 31.75 O HETATM 1714 O HOH A2062 6.253 38.590 43.073 1.00 17.69 O HETATM 1715 O HOH A2063 -1.619 24.653 44.765 1.00 28.56 O HETATM 1716 O HOH A2064 0.629 29.586 47.576 1.00 21.02 O HETATM 1717 O HOH A2065 2.580 29.346 49.600 1.00 21.09 O HETATM 1718 O HOH A2066 0.611 21.216 40.613 1.00 21.38 O HETATM 1719 O HOH A2067 1.185 22.895 44.561 1.00 25.80 O HETATM 1720 O HOH A2068 1.275 26.239 31.967 1.00 26.43 O HETATM 1721 O HOH A2069 0.071 29.044 38.277 1.00 18.61 O HETATM 1722 O HOH A2070 -0.286 28.053 33.145 1.00 35.80 O HETATM 1723 O HOH A2071 1.027 14.945 35.928 1.00 29.59 O HETATM 1724 O HOH A2072 -2.064 21.030 28.466 1.00 36.83 O HETATM 1725 O HOH B2001 1.080 5.738 26.914 1.00 28.58 O HETATM 1726 O HOH B2002 5.758 11.118 27.291 1.00 20.41 O HETATM 1727 O HOH B2003 5.638 12.526 24.803 1.00 24.97 O HETATM 1728 O HOH B2004 1.675 14.254 42.567 1.00 34.67 O HETATM 1729 O HOH B2005 9.397 18.373 55.454 1.00 27.47 O HETATM 1730 O HOH B2006 6.628 18.490 49.812 1.00 32.86 O HETATM 1731 O HOH B2007 11.446 12.329 60.815 1.00 27.96 O HETATM 1732 O HOH B2008 9.999 17.975 61.667 1.00 27.65 O HETATM 1733 O HOH B2009 16.089 13.617 49.248 1.00 34.74 O HETATM 1734 O HOH B2010 9.567 10.674 63.692 1.00 28.92 O HETATM 1735 O HOH B2011 4.372 13.267 64.955 1.00 24.43 O HETATM 1736 O HOH B2012 3.889 14.933 62.658 1.00 36.96 O HETATM 1737 O HOH B2013 9.928 12.455 67.515 1.00 16.94 O HETATM 1738 O HOH B2014 0.488 11.736 61.679 1.00 24.67 O HETATM 1739 O HOH B2015 -9.336 8.577 57.566 1.00 18.46 O HETATM 1740 O HOH B2016 -5.582 11.683 59.618 1.00 40.40 O HETATM 1741 O HOH B2017 -0.856 10.316 52.038 1.00 18.35 O HETATM 1742 O HOH B2018 -4.948 4.656 50.138 1.00 23.80 O HETATM 1743 O HOH B2019 -3.485 6.762 46.695 1.00 17.71 O HETATM 1744 O HOH B2020 -1.381 11.511 46.201 1.00 34.14 O HETATM 1745 O HOH B2021 -0.453 14.849 49.419 1.00 37.86 O HETATM 1746 O HOH B2022 -4.963 1.884 49.780 1.00 34.31 O HETATM 1747 O HOH B2023 -1.080 1.961 38.168 1.00 24.92 O HETATM 1748 O HOH B2024 0.363 -0.184 44.928 1.00 30.16 O HETATM 1749 O HOH B2025 0.311 9.921 39.810 1.00 28.66 O HETATM 1750 O HOH B2026 7.045 -0.597 36.500 1.00 18.00 O HETATM 1751 O HOH B2027 1.938 -0.220 43.264 1.00 14.16 O HETATM 1752 O HOH B2028 13.440 10.721 60.844 1.00 31.44 O HETATM 1753 O HOH B2029 9.160 3.485 30.272 1.00 34.31 O HETATM 1754 O HOH B2030 14.568 -1.074 31.631 1.00 31.18 O HETATM 1755 O HOH B2031 7.608 -2.314 34.023 1.00 26.24 O HETATM 1756 O HOH B2032 17.947 -2.460 39.980 1.00 32.59 O HETATM 1757 O HOH B2033 19.686 1.226 47.046 1.00 31.82 O HETATM 1758 O HOH B2034 22.691 -0.078 44.785 1.00 37.43 O HETATM 1759 O HOH B2035 13.186 2.974 43.123 1.00 15.76 O HETATM 1760 O HOH B2036 11.748 4.237 30.800 1.00 20.92 O HETATM 1761 O HOH B2037 10.058 -4.378 32.582 1.00 10.05 O HETATM 1762 O HOH B2038 11.463 -0.274 60.621 1.00 27.80 O HETATM 1763 O HOH B2039 6.075 -5.377 54.824 1.00 27.55 O HETATM 1764 O HOH B2040 1.693 -3.627 61.607 1.00 33.27 O HETATM 1765 O HOH B2041 8.778 -1.765 60.949 1.00 22.79 O HETATM 1766 O HOH B2042 -1.745 -3.147 62.570 1.00 26.24 O HETATM 1767 O HOH B2043 -4.179 -1.966 65.218 1.00 27.90 O HETATM 1768 O HOH B2044 -0.288 -1.211 63.885 1.00 32.62 O HETATM 1769 O HOH B2045 -5.985 -0.025 66.830 1.00 44.13 O HETATM 1770 O HOH B2046 -3.228 8.703 64.731 1.00 31.19 O HETATM 1771 O HOH B2047 -0.271 11.310 64.063 1.00 27.95 O HETATM 1772 O HOH B2048 12.131 9.647 63.564 1.00 29.12 O HETATM 1773 O HOH B2049 15.671 3.834 62.230 1.00 29.42 O HETATM 1774 O HOH B2050 3.837 1.078 64.250 1.00 33.66 O HETATM 1775 O HOH B2051 19.118 -0.086 57.066 1.00 31.09 O HETATM 1776 O HOH B2052 18.943 6.553 51.673 1.00 27.97 O HETATM 1777 O HOH B2053 15.021 1.591 48.937 1.00 29.53 O HETATM 1778 O HOH B2054 17.121 9.980 55.483 1.00 28.43 O HETATM 1779 O HOH B2055 19.242 8.688 54.034 1.00 24.11 O HETATM 1780 O HOH B2056 21.120 11.239 49.102 1.00 25.82 O HETATM 1781 O HOH B2057 16.900 1.188 47.293 1.00 33.03 O HETATM 1782 O HOH B2058 18.515 12.265 47.920 1.00 27.99 O HETATM 1783 O HOH B2059 20.667 9.462 42.367 1.00 16.05 O HETATM 1784 O HOH B2060 19.328 11.362 43.901 1.00 22.64 O HETATM 1785 O HOH B2061 19.923 3.926 46.227 1.00 18.27 O HETATM 1786 O HOH B2062 20.878 5.321 34.020 1.00 32.47 O MASTER 466 0 0 8 0 0 0 9 1772 2 0 16 END