HEADER PEPTIDE BINDING PROTEIN 15-AUG-14 4UWX TITLE STRUCTURE OF LIPRIN-ALPHA3 IN COMPLEX WITH MDIA1 DIAPHANOUS- TITLE 2 INHIBITORY DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN DIAPHANOUS HOMOLOG 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: DIAPHANOUS-INHIBITORY DOMAIN, RESIDUES 135-369; COMPND 5 SYNONYM: DIAPHANOUS-RELATED FORMIN-1, DRF1, P140MDIA, MDIA1, MDIA1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: LIPRIN-ALPHA-3; COMPND 9 CHAIN: C, D; COMPND 10 FRAGMENT: COILED-COIL DOMAIN; COMPND 11 SYNONYM: PROTEIN TYROSINE PHOSPHATASE RECEPTOR TYPE F POLYPEPTIDE-IN COMPND 12 TERACTING PROTEIN ALPHA-3, PTPRF-INTERACTING PROTEIN ALPHA-3, LIPR COMPND 13 IN-ALPHA3; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 9 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 10 ORGANISM_TAXID: 10090; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 13 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 14 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 15 EXPRESSION_SYSTEM_PLASMID: PGEX KEYWDS PEPTIDE-BINDING PROTEIN, ACTIN POLYMERISATION, RHOGNBPS, SYNAPE KEYWDS 2 MATURATION, CELL MOTILITY, FH1, FH2 DOMAIN, ACTIN-NUCLEATION FACTOR KEYWDS 3 - DIAPHANOUS-RELATED FORMIN, PEPTIDE BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.BRENIG,S.DE BOOR,P.KNYPHAUSEN,N.KUHLMANN,S.WROBLOWSKI,L.BALDUS, AUTHOR 2 L.SCISLOWSKI,O.ARTZ,P.TRAUSCHIES,U.BAUMANN,I.NEUNDORF,M.LAMMERS REVDAT 4 10-JAN-24 4UWX 1 REMARK LINK REVDAT 3 17-JUN-15 4UWX 1 JRNL REVDAT 2 13-MAY-15 4UWX 1 JRNL REVDAT 1 06-MAY-15 4UWX 0 JRNL AUTH J.BRENIG,S.DE BOOR,P.KNYPHAUSEN,N.KUHLMANN,S.WROBLOWSKI, JRNL AUTH 2 L.BALDUS,L.SCISLOWSKI,O.ARTZ,P.TRAUSCHIES,U.BAUMANN, JRNL AUTH 3 I.NEUNDORF,M.LAMMERS JRNL TITL STRUCTURAL AND BIOCHEMICAL BASIS FOR THE INHIBITORY EFFECT JRNL TITL 2 OF LIPRIN-ALPHA3 ON MOUSE DIAPHANOUS 1 (MDIA1) FUNCTION. JRNL REF J.BIOL.CHEM. V. 290 14314 2015 JRNL REFN ISSN 0021-9258 JRNL PMID 25911102 JRNL DOI 10.1074/JBC.M114.621946 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 75028 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3777 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5223 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.93 REMARK 3 BIN R VALUE (WORKING SET) : 0.3210 REMARK 3 BIN FREE R VALUE SET COUNT : 275 REMARK 3 BIN FREE R VALUE : 0.3610 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3926 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 393 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.92 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.06400 REMARK 3 B22 (A**2) : 2.16000 REMARK 3 B33 (A**2) : -2.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.13600 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.084 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.087 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.067 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.093 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3985 ; 0.022 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3965 ; 0.007 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5354 ; 2.005 ; 1.997 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9117 ; 1.316 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 489 ; 5.220 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 192 ;34.109 ;24.740 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 782 ;13.749 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;19.444 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 617 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4428 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 850 ; 0.005 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1439 ; 0.308 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 61 ; 0.295 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2037 ; 0.183 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 59 ; 0.195 ; 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 3985 ; 2.967 ; 1.891 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3965 ; 0.751 ; 1.975 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5354 ; 4.505 ; 2.759 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 516 ; 8.871 ; 6.067 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3395 ; 8.458 ;18.692 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 : 4 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 131 A 368 REMARK 3 ORIGIN FOR THE GROUP (A): 119.4759 -2.1112 136.3159 REMARK 3 T TENSOR REMARK 3 T11: 0.0739 T22: 0.0503 REMARK 3 T33: 0.0960 T12: 0.0165 REMARK 3 T13: -0.0030 T23: 0.0021 REMARK 3 L TENSOR REMARK 3 L11: 0.3261 L22: 0.1150 REMARK 3 L33: 0.5068 L12: -0.0494 REMARK 3 L13: -0.3266 L23: 0.1858 REMARK 3 S TENSOR REMARK 3 S11: 0.0035 S12: -0.0359 S13: 0.0021 REMARK 3 S21: -0.0007 S22: 0.0098 S23: -0.0154 REMARK 3 S31: 0.0013 S32: 0.0249 S33: -0.0133 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 : B 135 B 369 REMARK 3 ORIGIN FOR THE GROUP (A): 86.3814 3.8452 127.5499 REMARK 3 T TENSOR REMARK 3 T11: 0.0744 T22: 0.0427 REMARK 3 T33: 0.0984 T12: 0.0121 REMARK 3 T13: 0.0044 T23: -0.0011 REMARK 3 L TENSOR REMARK 3 L11: 0.3282 L22: 0.0217 REMARK 3 L33: 0.5409 L12: -0.0178 REMARK 3 L13: 0.3739 L23: 0.0034 REMARK 3 S TENSOR REMARK 3 S11: -0.0008 S12: -0.0234 S13: -0.0192 REMARK 3 S21: -0.0022 S22: 0.0087 S23: 0.0080 REMARK 3 S31: 0.0157 S32: 0.0076 S33: -0.0080 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 : C 567 C 581 REMARK 3 ORIGIN FOR THE GROUP (A): 124.8173 11.6560 148.5679 REMARK 3 T TENSOR REMARK 3 T11: 0.0794 T22: 0.1110 REMARK 3 T33: 0.1457 T12: -0.0635 REMARK 3 T13: 0.0440 T23: -0.0504 REMARK 3 L TENSOR REMARK 3 L11: 2.9638 L22: 4.6836 REMARK 3 L33: 5.7423 L12: -1.0686 REMARK 3 L13: -4.0612 L23: 1.3529 REMARK 3 S TENSOR REMARK 3 S11: 0.1839 S12: -0.2995 S13: 0.0995 REMARK 3 S21: -0.0214 S22: 0.1066 S23: -0.0010 REMARK 3 S31: -0.3603 S32: 0.4948 S33: -0.2904 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 : D 567 D 581 REMARK 3 ORIGIN FOR THE GROUP (A): 81.3074 -9.8234 116.0037 REMARK 3 T TENSOR REMARK 3 T11: 0.1297 T22: 0.0107 REMARK 3 T33: 0.1269 T12: 0.0209 REMARK 3 T13: -0.0014 T23: 0.0072 REMARK 3 L TENSOR REMARK 3 L11: 4.8297 L22: 1.0115 REMARK 3 L33: 3.4735 L12: 0.2248 REMARK 3 L13: 2.4264 L23: -0.0010 REMARK 3 S TENSOR REMARK 3 S11: 0.0906 S12: 0.1354 S13: -0.0339 REMARK 3 S21: 0.0649 S22: -0.0471 S23: -0.0298 REMARK 3 S31: 0.2419 S32: 0.1019 S33: -0.0434 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL PLUS MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 4UWX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1290060651. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : BARTELS SI (111) REMARK 200 OPTICS : MIRRORS TOROIDAL FOCUSSING REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : TRUNCATE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 75030 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 105.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.130 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.3700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.24 REMARK 200 R MERGE FOR SHELL (I) : 0.73000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.330 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: PDB ENTRY 1Z2C REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M NACL, 0.1 M TRIS/HCL PH 8.0, 20% REMARK 280 PEG6000 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 60.54500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.69050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 60.54500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.69050 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.3 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 GLU A 194 REMARK 465 GLU A 195 REMARK 465 THR A 196 REMARK 465 SER A 197 REMARK 465 GLY A 369 REMARK 465 GLY B 131 REMARK 465 SER B 132 REMARK 465 GLU B 133 REMARK 465 PHE B 134 REMARK 465 GLU B 194 REMARK 465 GLU B 195 REMARK 465 THR B 196 REMARK 465 SER B 197 REMARK 465 GLY B 198 REMARK 465 LEU C 582 REMARK 465 GLN C 583 REMARK 465 ALA C 584 REMARK 465 GLY C 585 REMARK 465 SER C 586 REMARK 465 PRO C 587 REMARK 465 GLN D 583 REMARK 465 ALA D 584 REMARK 465 GLY D 585 REMARK 465 SER D 586 REMARK 465 PRO D 587 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 O HOH A 2060 O HOH A 2061 0.90 REMARK 500 O HOH A 2050 O HOH A 2051 0.95 REMARK 500 O HOH A 2121 O HOH A 2122 0.99 REMARK 500 O HOH B 2122 O HOH B 2155 1.12 REMARK 500 O HOH B 2140 O HOH B 2143 1.18 REMARK 500 O HOH B 2156 O HOH B 2157 1.53 REMARK 500 CB SER A 181 O HOH A 2047 1.55 REMARK 500 SD MET B 266 O HOH B 2110 1.87 REMARK 500 SD MET A 266 O HOH A 2120 1.91 REMARK 500 O3 144 B 1371 O HOH A 2160 2.09 REMARK 500 O HOH A 2017 O HOH A 2019 2.12 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 2025 O HOH B 2114 3545 1.80 REMARK 500 O HOH A 2023 O HOH B 2125 3545 1.92 REMARK 500 O HOH A 2176 O HOH B 2008 2758 2.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLY A 131 C GLY A 131 O 0.125 REMARK 500 MET A 216 SD MET A 216 CE -0.500 REMARK 500 ARG B 160 CD ARG B 160 NE -0.124 REMARK 500 GLU B 318 CG GLU B 318 CD 0.092 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 160 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 MET A 216 CG - SD - CE ANGL. DEV. = -17.5 DEGREES REMARK 500 ARG A 269 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG B 160 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG B 160 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG B 237 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG B 326 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG B 331 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 ARG B 331 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG C 572 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG C 572 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG D 572 NE - CZ - NH1 ANGL. DEV. = 7.1 DEGREES REMARK 500 ARG D 572 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 MET D 576 CG - SD - CE ANGL. DEV. = -10.1 DEGREES 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 ASP A 149 -129.01 58.12 REMARK 500 GLU A 192 49.41 -100.64 REMARK 500 ASP B 149 -134.85 58.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B2038 DISTANCE = 6.44 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A1369 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 142 OE2 REMARK 620 2 HIS A 151 NE2 93.8 REMARK 620 3 144 A1370 O2 91.9 89.1 REMARK 620 4 144 A1370 O3 89.9 173.3 85.2 REMARK 620 5 144 A1370 O4 168.0 96.1 81.6 79.6 REMARK 620 6 HIS B 324 ND1 88.6 97.8 173.0 87.8 96.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B1370 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 324 ND1 REMARK 620 2 GLU B 142 OE2 93.6 REMARK 620 3 HIS B 151 NE2 97.2 92.4 REMARK 620 4 144 B1371 O4 95.9 169.4 91.1 REMARK 620 5 144 B1371 O3 68.9 105.4 157.7 73.8 REMARK 620 6 144 B1371 C3 100.2 93.1 161.4 80.6 33.2 REMARK 620 7 144 B1371 O2 171.5 87.0 91.2 83.0 102.8 71.4 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 1369 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 144 A 1370 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 1370 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 144 B 1371 DBREF 4UWX A 135 369 UNP O08808 DIAP1_MOUSE 135 369 DBREF 4UWX B 135 369 UNP O08808 DIAP1_MOUSE 135 369 DBREF 4UWX C 567 587 UNP P60469 LIPA3_MOUSE 567 587 DBREF 4UWX D 567 587 UNP P60469 LIPA3_MOUSE 567 587 SEQADV 4UWX GLY A 131 UNP O08808 EXPRESSION TAG SEQADV 4UWX SER A 132 UNP O08808 EXPRESSION TAG SEQADV 4UWX GLU A 133 UNP O08808 EXPRESSION TAG SEQADV 4UWX PHE A 134 UNP O08808 EXPRESSION TAG SEQADV 4UWX GLY B 131 UNP O08808 EXPRESSION TAG SEQADV 4UWX SER B 132 UNP O08808 EXPRESSION TAG SEQADV 4UWX GLU B 133 UNP O08808 EXPRESSION TAG SEQADV 4UWX PHE B 134 UNP O08808 EXPRESSION TAG SEQRES 1 A 239 GLY SER GLU PHE SER ALA MET MET TYR ILE GLN GLU LEU SEQRES 2 A 239 ARG SER GLY LEU ARG ASP MET HIS LEU LEU SER CYS LEU SEQRES 3 A 239 GLU SER LEU ARG VAL SER LEU ASN ASN ASN PRO VAL SER SEQRES 4 A 239 TRP VAL GLN THR PHE GLY ALA GLU GLY LEU ALA SER LEU SEQRES 5 A 239 LEU ASP ILE LEU LYS ARG LEU HIS ASP GLU LYS GLU GLU SEQRES 6 A 239 THR SER GLY ASN TYR ASP SER ARG ASN GLN HIS GLU ILE SEQRES 7 A 239 ILE ARG CYS LEU LYS ALA PHE MET ASN ASN LYS PHE GLY SEQRES 8 A 239 ILE LYS THR MET LEU GLU THR GLU GLU GLY ILE LEU LEU SEQRES 9 A 239 LEU VAL ARG ALA MET ASP PRO ALA VAL PRO ASN MET MET SEQRES 10 A 239 ILE ASP ALA ALA LYS LEU LEU SER ALA LEU CYS ILE LEU SEQRES 11 A 239 PRO GLN PRO GLU ASP MET ASN GLU ARG VAL LEU GLU ALA SEQRES 12 A 239 MET THR GLU ARG ALA GLU MET ASP GLU VAL GLU ARG PHE SEQRES 13 A 239 GLN PRO LEU LEU ASP GLY LEU LYS SER GLY THR SER ILE SEQRES 14 A 239 ALA LEU LYS VAL GLY CYS LEU GLN LEU ILE ASN ALA LEU SEQRES 15 A 239 ILE THR PRO ALA GLU GLU LEU ASP PHE ARG VAL HIS ILE SEQRES 16 A 239 ARG SER GLU LEU MET ARG LEU GLY LEU HIS GLN VAL LEU SEQRES 17 A 239 GLN GLU LEU ARG GLU ILE GLU ASN GLU ASP MET LYS VAL SEQRES 18 A 239 GLN LEU CYS VAL PHE ASP GLU GLN GLY ASP GLU ASP PHE SEQRES 19 A 239 PHE ASP LEU LYS GLY SEQRES 1 B 239 GLY SER GLU PHE SER ALA MET MET TYR ILE GLN GLU LEU SEQRES 2 B 239 ARG SER GLY LEU ARG ASP MET HIS LEU LEU SER CYS LEU SEQRES 3 B 239 GLU SER LEU ARG VAL SER LEU ASN ASN ASN PRO VAL SER SEQRES 4 B 239 TRP VAL GLN THR PHE GLY ALA GLU GLY LEU ALA SER LEU SEQRES 5 B 239 LEU ASP ILE LEU LYS ARG LEU HIS ASP GLU LYS GLU GLU SEQRES 6 B 239 THR SER GLY ASN TYR ASP SER ARG ASN GLN HIS GLU ILE SEQRES 7 B 239 ILE ARG CYS LEU LYS ALA PHE MET ASN ASN LYS PHE GLY SEQRES 8 B 239 ILE LYS THR MET LEU GLU THR GLU GLU GLY ILE LEU LEU SEQRES 9 B 239 LEU VAL ARG ALA MET ASP PRO ALA VAL PRO ASN MET MET SEQRES 10 B 239 ILE ASP ALA ALA LYS LEU LEU SER ALA LEU CYS ILE LEU SEQRES 11 B 239 PRO GLN PRO GLU ASP MET ASN GLU ARG VAL LEU GLU ALA SEQRES 12 B 239 MET THR GLU ARG ALA GLU MET ASP GLU VAL GLU ARG PHE SEQRES 13 B 239 GLN PRO LEU LEU ASP GLY LEU LYS SER GLY THR SER ILE SEQRES 14 B 239 ALA LEU LYS VAL GLY CYS LEU GLN LEU ILE ASN ALA LEU SEQRES 15 B 239 ILE THR PRO ALA GLU GLU LEU ASP PHE ARG VAL HIS ILE SEQRES 16 B 239 ARG SER GLU LEU MET ARG LEU GLY LEU HIS GLN VAL LEU SEQRES 17 B 239 GLN GLU LEU ARG GLU ILE GLU ASN GLU ASP MET LYS VAL SEQRES 18 B 239 GLN LEU CYS VAL PHE ASP GLU GLN GLY ASP GLU ASP PHE SEQRES 19 B 239 PHE ASP LEU LYS GLY SEQRES 1 C 21 THR PRO ARG SER ALA ARG LEU GLU ARG MET ALA GLN ALA SEQRES 2 C 21 LEU ALA LEU GLN ALA GLY SER PRO SEQRES 1 D 21 THR PRO ARG SER ALA ARG LEU GLU ARG MET ALA GLN ALA SEQRES 2 D 21 LEU ALA LEU GLN ALA GLY SER PRO HET NI A1369 1 HET 144 A1370 8 HET NI B1370 1 HET 144 B1371 8 HETNAM NI NICKEL (II) ION HETNAM 144 TRIS-HYDROXYMETHYL-METHYL-AMMONIUM FORMUL 5 NI 2(NI 2+) FORMUL 6 144 2(C4 H12 N O3 1+) FORMUL 9 HOH *393(H2 O) HELIX 1 1 SER A 132 ARG A 144 1 13 HELIX 2 2 ARG A 148 ASN A 166 1 19 HELIX 3 3 PRO A 167 GLU A 192 1 26 HELIX 4 4 TYR A 200 MET A 216 1 17 HELIX 5 5 ASN A 218 GLU A 227 1 10 HELIX 6 6 GLU A 230 ALA A 238 1 9 HELIX 7 7 VAL A 243 ILE A 259 1 17 HELIX 8 8 ASP A 265 GLU A 282 1 18 HELIX 9 9 PHE A 286 LEU A 293 1 8 HELIX 10 10 SER A 298 THR A 314 1 17 HELIX 11 11 GLU A 318 GLY A 333 1 16 HELIX 12 12 GLY A 333 GLU A 343 1 11 HELIX 13 13 ASN A 346 LYS A 368 1 23 HELIX 14 14 SER B 135 SER B 145 1 11 HELIX 15 15 ARG B 148 ASN B 166 1 19 HELIX 16 16 PRO B 167 GLU B 192 1 26 HELIX 17 17 TYR B 200 MET B 216 1 17 HELIX 18 18 ASN B 218 THR B 228 1 11 HELIX 19 19 GLU B 230 ALA B 238 1 9 HELIX 20 20 VAL B 243 ILE B 259 1 17 HELIX 21 21 ASP B 265 GLU B 282 1 18 HELIX 22 22 PHE B 286 LEU B 293 1 8 HELIX 23 23 SER B 298 THR B 314 1 17 HELIX 24 24 GLU B 318 LEU B 332 1 15 HELIX 25 25 GLY B 333 ARG B 342 1 10 HELIX 26 26 ASN B 346 GLY B 369 1 24 HELIX 27 27 THR C 567 ALA C 581 1 15 HELIX 28 28 THR D 567 LEU D 582 1 16 LINK OE2 GLU A 142 NI NI A1369 1555 1555 2.10 LINK NE2 HIS A 151 NI NI A1369 1555 1555 2.19 LINK ND1 HIS A 324 NI NI B1370 1555 1555 2.17 LINK NI NI A1369 O2 144 A1370 1555 1555 2.18 LINK NI NI A1369 O3 144 A1370 1555 1555 2.14 LINK NI NI A1369 O4 144 A1370 1555 1555 2.18 LINK NI NI A1369 ND1 HIS B 324 1555 3545 2.24 LINK OE2 GLU B 142 NI NI B1370 1555 1555 2.05 LINK NE2 HIS B 151 NI NI B1370 1555 1555 2.11 LINK NI NI B1370 O4 144 B1371 1555 1555 2.23 LINK NI NI B1370 O3 144 B1371 1555 1555 2.47 LINK NI NI B1370 C3 144 B1371 1555 1555 2.28 LINK NI NI B1370 O2 144 B1371 1555 1555 2.24 CISPEP 1 GLY A 131 SER A 132 0 4.43 CISPEP 2 GLN A 262 PRO A 263 0 -9.94 CISPEP 3 GLN B 262 PRO B 263 0 -10.54 SITE 1 AC1 4 GLU A 142 HIS A 151 144 A1370 HIS B 324 SITE 1 AC2 5 GLU A 142 HIS A 151 NI A1369 HOH A2020 SITE 2 AC2 5 HIS B 324 SITE 1 AC3 4 HIS A 324 GLU B 142 HIS B 151 144 B1371 SITE 1 AC4 7 HIS A 324 ARG A 331 HOH A2157 HOH A2160 SITE 2 AC4 7 GLU B 142 HIS B 151 NI B1370 CRYST1 121.090 49.381 106.370 90.00 97.86 90.00 C 1 2 1 8 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 0.008258 0.000000 0.001140 0.00000 SCALE2 0.000000 0.020251 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009490 0.00000