HEADER PROTEIN TRANSPORT 09-MAY-11 3RWO TITLE CRYSTAL STRUCTURE OF YPT32 IN COMPLEX WITH GDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: GTP-BINDING PROTEIN YPT32/YPT11; COMPND 3 CHAIN: B, A; COMPND 4 SYNONYM: RAB GTPASE YPT32; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: ATCC 204508 / S288C; SOURCE 6 GENE: YGL210W, YPT11, YPT32; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS GTPASES, PROTEIN-GDP COMPLEX, EXOCYTOSIS, GOLGI APPARATUS, GTP- KEYWDS 2 BINDING, LIPOPROTEIN, MEMBRANE, NUCLEOTIDE-BINDING, PRENYLATION, KEYWDS 3 PROTEIN TRANSPORT, TRANSPORT, YPT32, RAB GTPASE, GDP, VESICLE KEYWDS 4 TRAFFICKING, MYO2P, EFFECTORS EXPDTA X-RAY DIFFRACTION AUTHOR A.SULTANA,Y.JIN,C.DREGGER,E.FRANKLIN,L.S.WEISMAN,A.R.KHAN REVDAT 4 13-SEP-23 3RWO 1 REMARK SEQADV LINK REVDAT 3 14-DEC-11 3RWO 1 JRNL REVDAT 2 09-NOV-11 3RWO 1 JRNL REVDAT 1 26-OCT-11 3RWO 0 JRNL AUTH A.SULTANA,Y.JIN,C.DREGGER,E.FRANKLIN,L.S.WEISMAN,A.R.KHAN JRNL TITL THE ACTIVATION CYCLE OF RAB GTPASE YPT32 REVEALS STRUCTURAL JRNL TITL 2 DETERMINANTS OF EFFECTOR RECRUITMENT AND GDI BINDING. JRNL REF FEBS LETT. V. 585 3520 2011 JRNL REFN ISSN 0014-5793 JRNL PMID 22024479 JRNL DOI 10.1016/J.FEBSLET.2011.10.013 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0044 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 68.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 44104 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) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2223 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3087 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.2420 REMARK 3 BIN FREE R VALUE SET COUNT : 156 REMARK 3 BIN FREE R VALUE : 0.2840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2700 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 495 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.66 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.37000 REMARK 3 B22 (A**2) : 0.15000 REMARK 3 B33 (A**2) : 0.17000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.08000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.099 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.059 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.362 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2907 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3984 ; 1.333 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 380 ; 5.753 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 143 ;37.159 ;25.035 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 495 ;14.316 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;18.007 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 461 ; 0.109 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2208 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1757 ; 0.778 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2847 ; 1.418 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1150 ; 1.944 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1115 ; 3.029 ; 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 : 7 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 10 A 35 REMARK 3 RESIDUE RANGE : B 10 B 35 REMARK 3 ORIGIN FOR THE GROUP (A): 2.9090 -7.3030 45.4070 REMARK 3 T TENSOR REMARK 3 T11: 0.0243 T22: 0.0106 REMARK 3 T33: 0.0322 T12: -0.0012 REMARK 3 T13: -0.0081 T23: -0.0098 REMARK 3 L TENSOR REMARK 3 L11: 0.3109 L22: 0.2973 REMARK 3 L33: 0.6786 L12: -0.0817 REMARK 3 L13: -0.2808 L23: -0.1090 REMARK 3 S TENSOR REMARK 3 S11: 0.0272 S12: 0.0094 S13: 0.0078 REMARK 3 S21: 0.0045 S22: -0.0376 S23: -0.0198 REMARK 3 S31: 0.0306 S32: 0.0048 S33: 0.0103 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 36 A 47 REMARK 3 ORIGIN FOR THE GROUP (A): 9.8920 -9.7450 53.7750 REMARK 3 T TENSOR REMARK 3 T11: 0.1190 T22: 0.0848 REMARK 3 T33: 0.1306 T12: -0.0189 REMARK 3 T13: 0.0190 T23: 0.0158 REMARK 3 L TENSOR REMARK 3 L11: 1.8654 L22: 1.1672 REMARK 3 L33: 1.9537 L12: -1.4532 REMARK 3 L13: 1.5112 L23: -1.3300 REMARK 3 S TENSOR REMARK 3 S11: -0.0487 S12: 0.1561 S13: 0.3560 REMARK 3 S21: -0.0007 S22: -0.1744 S23: -0.2757 REMARK 3 S31: 0.0129 S32: 0.3139 S33: 0.2231 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 : B 36 B 47 REMARK 3 ORIGIN FOR THE GROUP (A): 11.8420 -8.9600 41.5860 REMARK 3 T TENSOR REMARK 3 T11: 0.2305 T22: 0.1221 REMARK 3 T33: 0.0962 T12: -0.0023 REMARK 3 T13: -0.0261 T23: -0.0068 REMARK 3 L TENSOR REMARK 3 L11: 5.6658 L22: 0.8177 REMARK 3 L33: 0.4522 L12: 1.4315 REMARK 3 L13: -1.1633 L23: -0.5748 REMARK 3 S TENSOR REMARK 3 S11: 0.0368 S12: -0.4353 S13: -0.2696 REMARK 3 S21: 0.1780 S22: -0.1581 S23: -0.1692 REMARK 3 S31: -0.0294 S32: 0.1336 S33: 0.1213 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 48 A 68 REMARK 3 RESIDUE RANGE : B 48 B 68 REMARK 3 ORIGIN FOR THE GROUP (A): 1.4690 -6.1480 44.4270 REMARK 3 T TENSOR REMARK 3 T11: 0.0375 T22: 0.0209 REMARK 3 T33: 0.0342 T12: 0.0003 REMARK 3 T13: -0.0035 T23: -0.0097 REMARK 3 L TENSOR REMARK 3 L11: 0.6055 L22: 1.3292 REMARK 3 L33: 0.9289 L12: 0.2993 REMARK 3 L13: -0.3405 L23: -0.7678 REMARK 3 S TENSOR REMARK 3 S11: 0.0559 S12: 0.0557 S13: -0.0122 REMARK 3 S21: -0.0096 S22: -0.0675 S23: -0.0567 REMARK 3 S31: 0.0431 S32: -0.0007 S33: 0.0115 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 69 A 78 REMARK 3 RESIDUE RANGE : B 69 B 78 REMARK 3 ORIGIN FOR THE GROUP (A): -6.4540 -4.5510 43.7970 REMARK 3 T TENSOR REMARK 3 T11: 0.0288 T22: 0.1721 REMARK 3 T33: 0.0805 T12: -0.0293 REMARK 3 T13: -0.0025 T23: -0.0079 REMARK 3 L TENSOR REMARK 3 L11: 3.0462 L22: 1.7770 REMARK 3 L33: 1.0183 L12: -0.3546 REMARK 3 L13: -0.0470 L23: -1.0430 REMARK 3 S TENSOR REMARK 3 S11: -0.0340 S12: 0.1690 S13: 0.0507 REMARK 3 S21: 0.0653 S22: 0.0571 S23: 0.0719 REMARK 3 S31: 0.0135 S32: -0.2984 S33: -0.0232 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 79 A 112 REMARK 3 RESIDUE RANGE : B 79 B 112 REMARK 3 ORIGIN FOR THE GROUP (A): -3.0280 -6.2720 44.4620 REMARK 3 T TENSOR REMARK 3 T11: 0.0101 T22: 0.0358 REMARK 3 T33: 0.0545 T12: 0.0044 REMARK 3 T13: -0.0096 T23: -0.0115 REMARK 3 L TENSOR REMARK 3 L11: 0.4730 L22: 0.5493 REMARK 3 L33: 1.4015 L12: -0.0334 REMARK 3 L13: -0.2280 L23: -0.1742 REMARK 3 S TENSOR REMARK 3 S11: 0.0489 S12: 0.0592 S13: 0.0092 REMARK 3 S21: 0.0206 S22: 0.0092 S23: 0.0357 REMARK 3 S31: 0.0153 S32: -0.1935 S33: -0.0581 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 121 A 178 REMARK 3 RESIDUE RANGE : B 121 B 178 REMARK 3 ORIGIN FOR THE GROUP (A): 5.0750 -8.6730 45.4530 REMARK 3 T TENSOR REMARK 3 T11: 0.0102 T22: 0.0091 REMARK 3 T33: 0.0381 T12: 0.0028 REMARK 3 T13: -0.0119 T23: -0.0089 REMARK 3 L TENSOR REMARK 3 L11: 0.5708 L22: 0.6250 REMARK 3 L33: 0.8295 L12: -0.1182 REMARK 3 L13: -0.0938 L23: 0.1009 REMARK 3 S TENSOR REMARK 3 S11: 0.0476 S12: 0.0265 S13: -0.0056 REMARK 3 S21: 0.0226 S22: -0.0566 S23: -0.0299 REMARK 3 S31: 0.0319 S32: -0.0088 S33: 0.0090 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3RWO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAY-11. REMARK 100 THE DEPOSITION ID IS D_1000065469. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-FEB-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97849 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44104 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 68.750 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.40100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3CPJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, MGCL2, PH 8.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 65.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.60000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 65.00000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.60000 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, 3 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 300 REMARK: AUTHORS STATE THAT THE QUATERNARY STRUCTURE OF YPT32 IN REMARK 300 SOLUTION IS A MONOMER. THE DIMER THAT WAS OBSERVED IN THE STRUCTURE REMARK 300 IS A RESULT OF CRYSTALLOGRAPHIC PACKING. 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 GLY B 4 REMARK 465 ALA B 5 REMARK 465 MET B 6 REMARK 465 SER B 179 REMARK 465 LYS B 180 REMARK 465 HIS B 181 REMARK 465 GLN B 182 REMARK 465 VAL B 183 REMARK 465 ASP B 184 REMARK 465 LEU B 185 REMARK 465 SER B 186 REMARK 465 GLY B 187 REMARK 465 SER B 188 REMARK 465 GLY A 4 REMARK 465 ALA A 5 REMARK 465 MET A 6 REMARK 465 GLY A 7 REMARK 465 TYR A 8 REMARK 465 SER A 179 REMARK 465 LYS A 180 REMARK 465 HIS A 181 REMARK 465 GLN A 182 REMARK 465 VAL A 183 REMARK 465 ASP A 184 REMARK 465 LEU A 185 REMARK 465 SER A 186 REMARK 465 GLY A 187 REMARK 465 SER A 188 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS B 43 CG CD CE NZ REMARK 480 ARG B 74 CG CD NE CZ NH1 NH2 REMARK 480 ASN B 118 CG OD1 ND2 REMARK 480 GLU A 41 CG CD OE1 OE2 REMARK 480 LYS A 43 CG CD CE NZ REMARK 480 LYS A 61 NZ REMARK 480 ARG A 76 CD NH1 REMARK 480 ASP A 117 CG OD1 OD2 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 NZ LYS B 43 O HOH B 277 1.87 REMARK 500 O HOH A 355 O HOH A 357 2.03 REMARK 500 O HOH A 260 O HOH A 355 2.08 REMARK 500 O HOH A 267 O HOH A 355 2.08 REMARK 500 O HOH A 355 O HOH A 358 2.08 REMARK 500 O HOH B 317 O HOH B 512 2.09 REMARK 500 O HOH A 355 O HOH A 359 2.15 REMARK 500 OE1 GLU B 102 O HOH B 552 2.19 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 B 248 O HOH B 528 2556 2.09 REMARK 500 O HOH A 355 O HOH A 356 4547 2.11 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 ASN B 59 12.56 59.42 REMARK 500 ASN B 59 12.49 59.74 REMARK 500 LEU B 130 43.49 -93.88 REMARK 500 SER B 160 -14.87 87.28 REMARK 500 SER B 160 -10.83 84.22 REMARK 500 SER A 44 46.51 -105.86 REMARK 500 LEU A 130 36.05 -96.65 REMARK 500 SER A 160 -13.23 82.58 REMARK 500 REMARK 500 REMARK: NULL 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 MG B1176 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 27 OG REMARK 620 2 HOH B 209 O 86.6 REMARK 620 3 HOH B 464 O 87.8 86.0 REMARK 620 4 HOH B 465 O 86.7 90.1 173.5 REMARK 620 5 HOH B 466 O 175.3 88.8 92.6 92.6 REMARK 620 6 GDP B4032 O3B 89.9 174.3 89.4 94.1 94.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1175 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 27 OG REMARK 620 2 HOH A 194 O 89.0 REMARK 620 3 HOH A 461 O 91.0 85.6 REMARK 620 4 HOH A 462 O 89.6 91.0 176.6 REMARK 620 5 HOH A 463 O 178.5 90.2 90.2 89.1 REMARK 620 6 GDP A4032 O3B 90.4 173.6 88.1 95.3 90.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP B 4032 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1176 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP A 4032 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1175 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3RWM RELATED DB: PDB REMARK 900 STRUCTURE OF YPT32 WITH GPPNHP DBREF 3RWO B 7 188 UNP P51996 YPT32_YEAST 7 188 DBREF 3RWO A 7 188 UNP P51996 YPT32_YEAST 7 188 SEQADV 3RWO GLY B 4 UNP P51996 EXPRESSION TAG SEQADV 3RWO ALA B 5 UNP P51996 EXPRESSION TAG SEQADV 3RWO MET B 6 UNP P51996 EXPRESSION TAG SEQADV 3RWO LEU B 72 UNP P51996 GLN 72 ENGINEERED MUTATION SEQADV 3RWO GLY A 4 UNP P51996 EXPRESSION TAG SEQADV 3RWO ALA A 5 UNP P51996 EXPRESSION TAG SEQADV 3RWO MET A 6 UNP P51996 EXPRESSION TAG SEQADV 3RWO LEU A 72 UNP P51996 GLN 72 ENGINEERED MUTATION SEQRES 1 B 185 GLY ALA MET GLY TYR ASP TYR ASP TYR LEU PHE LYS ILE SEQRES 2 B 185 VAL LEU ILE GLY ASP SER GLY VAL GLY LYS SER ASN LEU SEQRES 3 B 185 LEU SER ARG PHE THR THR ASP GLU PHE ASN ILE GLU SER SEQRES 4 B 185 LYS SER THR ILE GLY VAL GLU PHE ALA THR ARG THR ILE SEQRES 5 B 185 GLU VAL GLU ASN LYS LYS ILE LYS ALA GLN ILE TRP ASP SEQRES 6 B 185 THR ALA GLY LEU GLU ARG TYR ARG ALA ILE THR SER ALA SEQRES 7 B 185 TYR TYR ARG GLY ALA VAL GLY ALA LEU ILE VAL TYR ASP SEQRES 8 B 185 ILE SER LYS SER SER SER TYR GLU ASN CYS ASN HIS TRP SEQRES 9 B 185 LEU THR GLU LEU ARG GLU ASN ALA ASP ASP ASN VAL ALA SEQRES 10 B 185 VAL GLY LEU ILE GLY ASN LYS SER ASP LEU ALA HIS LEU SEQRES 11 B 185 ARG ALA VAL PRO THR ASP GLU ALA LYS ASN PHE ALA MET SEQRES 12 B 185 GLU ASN GLN MET LEU PHE THR GLU THR SER ALA LEU ASN SEQRES 13 B 185 SER ASP ASN VAL ASP LYS ALA PHE ARG GLU LEU ILE VAL SEQRES 14 B 185 ALA ILE PHE GLN MET VAL SER LYS HIS GLN VAL ASP LEU SEQRES 15 B 185 SER GLY SER SEQRES 1 A 185 GLY ALA MET GLY TYR ASP TYR ASP TYR LEU PHE LYS ILE SEQRES 2 A 185 VAL LEU ILE GLY ASP SER GLY VAL GLY LYS SER ASN LEU SEQRES 3 A 185 LEU SER ARG PHE THR THR ASP GLU PHE ASN ILE GLU SER SEQRES 4 A 185 LYS SER THR ILE GLY VAL GLU PHE ALA THR ARG THR ILE SEQRES 5 A 185 GLU VAL GLU ASN LYS LYS ILE LYS ALA GLN ILE TRP ASP SEQRES 6 A 185 THR ALA GLY LEU GLU ARG TYR ARG ALA ILE THR SER ALA SEQRES 7 A 185 TYR TYR ARG GLY ALA VAL GLY ALA LEU ILE VAL TYR ASP SEQRES 8 A 185 ILE SER LYS SER SER SER TYR GLU ASN CYS ASN HIS TRP SEQRES 9 A 185 LEU THR GLU LEU ARG GLU ASN ALA ASP ASP ASN VAL ALA SEQRES 10 A 185 VAL GLY LEU ILE GLY ASN LYS SER ASP LEU ALA HIS LEU SEQRES 11 A 185 ARG ALA VAL PRO THR ASP GLU ALA LYS ASN PHE ALA MET SEQRES 12 A 185 GLU ASN GLN MET LEU PHE THR GLU THR SER ALA LEU ASN SEQRES 13 A 185 SER ASP ASN VAL ASP LYS ALA PHE ARG GLU LEU ILE VAL SEQRES 14 A 185 ALA ILE PHE GLN MET VAL SER LYS HIS GLN VAL ASP LEU SEQRES 15 A 185 SER GLY SER HET GDP B4032 28 HET MG B1176 1 HET GDP A4032 28 HET MG A1175 1 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 3 GDP 2(C10 H15 N5 O11 P2) FORMUL 4 MG 2(MG 2+) FORMUL 7 HOH *495(H2 O) HELIX 1 1 GLY B 25 ASP B 36 1 12 HELIX 2 2 TYR B 75 ARG B 84 1 10 HELIX 3 3 LYS B 97 ASN B 103 1 7 HELIX 4 4 ASN B 103 ALA B 115 1 13 HELIX 5 5 LYS B 127 ARG B 134 5 8 HELIX 6 6 PRO B 137 ASN B 148 1 12 HELIX 7 7 ASN B 162 VAL B 178 1 17 HELIX 8 8 GLY A 25 ASP A 36 1 12 HELIX 9 9 TYR A 75 ARG A 84 1 10 HELIX 10 10 LYS A 97 ASN A 103 1 7 HELIX 11 11 ASN A 103 ALA A 115 1 13 HELIX 12 12 LYS A 127 ARG A 134 5 8 HELIX 13 13 PRO A 137 ASN A 148 1 12 HELIX 14 14 ASN A 162 VAL A 178 1 17 SHEET 1 A12 LEU B 151 GLU B 154 0 SHEET 2 A12 ALA B 120 ASN B 126 1 N LEU B 123 O LEU B 151 SHEET 3 A12 GLY B 88 ASP B 94 1 N TYR B 93 O ASN B 126 SHEET 4 A12 TYR B 12 ILE B 19 1 N ILE B 19 O VAL B 92 SHEET 5 A12 LYS B 60 ALA B 70 1 O TRP B 67 N ILE B 16 SHEET 6 A12 GLY B 47 VAL B 57 -1 N ILE B 55 O ILE B 62 SHEET 7 A12 ILE A 46 VAL A 57 -1 O VAL A 48 N VAL B 48 SHEET 8 A12 LYS A 60 ALA A 70 -1 O ILE A 62 N ILE A 55 SHEET 9 A12 TYR A 12 GLY A 20 1 N ILE A 16 O TRP A 67 SHEET 10 A12 GLY A 88 ASP A 94 1 O VAL A 92 N ILE A 19 SHEET 11 A12 ALA A 120 ASN A 126 1 O ASN A 126 N TYR A 93 SHEET 12 A12 LEU A 151 GLU A 154 1 O LEU A 151 N LEU A 123 LINK OG SER B 27 MG MG B1176 1555 1555 2.13 LINK O HOH B 209 MG MG B1176 1555 1555 2.19 LINK O HOH B 464 MG MG B1176 1555 1555 2.16 LINK O HOH B 465 MG MG B1176 1555 1555 2.11 LINK O HOH B 466 MG MG B1176 1555 1555 2.13 LINK MG MG B1176 O3B GDP B4032 1555 1555 2.01 LINK OG SER A 27 MG MG A1175 1555 1555 2.06 LINK O HOH A 194 MG MG A1175 1555 1555 2.16 LINK O HOH A 461 MG MG A1175 1555 1555 2.09 LINK O HOH A 462 MG MG A1175 1555 1555 2.10 LINK O HOH A 463 MG MG A1175 1555 1555 2.21 LINK MG MG A1175 O3B GDP A4032 1555 1555 2.00 SITE 1 AC1 29 GLY B 23 VAL B 24 GLY B 25 LYS B 26 SITE 2 AC1 29 SER B 27 ASN B 28 PHE B 38 ASN B 39 SITE 3 AC1 29 ILE B 40 GLU B 41 SER B 42 ASN B 126 SITE 4 AC1 29 LYS B 127 ASP B 129 LEU B 130 SER B 156 SITE 5 AC1 29 ALA B 157 LEU B 158 HOH B 196 HOH B 233 SITE 6 AC1 29 HOH B 318 HOH B 325 HOH B 334 HOH B 464 SITE 7 AC1 29 HOH B 465 HOH B 466 HOH B 545 HOH B 561 SITE 8 AC1 29 MG B1176 SITE 1 AC2 6 SER B 27 HOH B 209 HOH B 464 HOH B 465 SITE 2 AC2 6 HOH B 466 GDP B4032 SITE 1 AC3 25 GLY A 23 VAL A 24 GLY A 25 LYS A 26 SITE 2 AC3 25 SER A 27 ASN A 28 PHE A 38 ASN A 39 SITE 3 AC3 25 ILE A 40 ASN A 126 LYS A 127 ASP A 129 SITE 4 AC3 25 LEU A 130 SER A 156 ALA A 157 LEU A 158 SITE 5 AC3 25 HOH A 240 HOH A 269 HOH A 271 HOH A 279 SITE 6 AC3 25 HOH A 415 HOH A 461 HOH A 462 HOH A 463 SITE 7 AC3 25 MG A1175 SITE 1 AC4 6 SER A 27 HOH A 194 HOH A 461 HOH A 462 SITE 2 AC4 6 HOH A 463 GDP A4032 CRYST1 130.000 45.200 73.400 90.00 110.50 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 0.007692 0.000000 0.002876 0.00000 SCALE2 0.000000 0.022124 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014545 0.00000