HEADER GTP BINDING PROTEIN 20-APR-15 4ZDW TITLE CRYSTAL STRUCTURE OF THE RAB GTPASE SEC4P MUTANT - S29V IN COMPLEX TITLE 2 WITH SEC2P AND GDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN SEC4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SUPPRESSOR OF RHO3 PROTEIN 6; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RAB GUANINE NUCLEOTIDE EXCHANGE FACTOR SEC2; COMPND 9 CHAIN: B, C; COMPND 10 SYNONYM: GDP-GTP EXCHANGE FACTOR SEC2; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / SOURCE 3 S288C); SOURCE 4 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 5 ORGANISM_TAXID: 559292; SOURCE 6 STRAIN: ATCC 204508 / S288C; SOURCE 7 GENE: SEC4, SRO6, YFL005W; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PPSUMO; SOURCE 13 MOL_ID: 2; SOURCE 14 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / SOURCE 15 S288C); SOURCE 16 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 17 ORGANISM_TAXID: 559292; SOURCE 18 STRAIN: ATCC 204508 / S288C; SOURCE 19 GENE: SEC2, YNL272C, N0641; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 22 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS GTPASE, GDP BOUND, RAB SEC4P, SEC2P, GTP BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.C.RINADI,R.N.COLLINS REVDAT 5 27-SEP-23 4ZDW 1 REMARK REVDAT 4 25-DEC-19 4ZDW 1 REMARK REVDAT 3 01-NOV-17 4ZDW 1 REMARK REVDAT 2 20-SEP-17 4ZDW 1 REMARK REVDAT 1 14-OCT-15 4ZDW 0 JRNL AUTH F.C.RINALDI,M.PACKER,R.COLLINS JRNL TITL NEW INSIGHTS INTO THE MOLECULAR MECHANISM OF THE RAB GTPASE JRNL TITL 2 SEC4P ACTIVATION. JRNL REF BMC STRUCT.BIOL. V. 15 14 2015 JRNL REFN ESSN 1472-6807 JRNL PMID 26263895 JRNL DOI 10.1186/S12900-015-0041-5 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 85.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 89.5 REMARK 3 NUMBER OF REFLECTIONS : 16492 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) : 0.260 REMARK 3 R VALUE (WORKING SET) : 0.258 REMARK 3 FREE R VALUE : 0.295 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 879 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) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 385 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 29.73 REMARK 3 BIN R VALUE (WORKING SET) : 0.3260 REMARK 3 BIN FREE R VALUE SET COUNT : 22 REMARK 3 BIN FREE R VALUE : 0.5120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2823 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 16 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 68.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.33000 REMARK 3 B22 (A**2) : 0.65000 REMARK 3 B33 (A**2) : -0.32000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.597 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.377 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.337 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 38.788 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.893 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.869 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2876 ; 0.012 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3867 ; 1.613 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 344 ; 7.092 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 154 ;36.958 ;25.649 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 576 ;22.267 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;22.777 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 442 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2117 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 3 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 20 A 186 REMARK 3 ORIGIN FOR THE GROUP (A): -25.7645 -22.6123 -18.6267 REMARK 3 T TENSOR REMARK 3 T11: 0.2574 T22: 0.6052 REMARK 3 T33: 0.3454 T12: 0.1060 REMARK 3 T13: 0.0837 T23: -0.1057 REMARK 3 L TENSOR REMARK 3 L11: 4.0513 L22: 1.8347 REMARK 3 L33: 4.5812 L12: -0.3474 REMARK 3 L13: -1.7720 L23: 0.1746 REMARK 3 S TENSOR REMARK 3 S11: 0.1013 S12: 0.6896 S13: -0.1678 REMARK 3 S21: -0.4318 S22: 0.1287 S23: -0.5856 REMARK 3 S31: -0.1002 S32: 0.5966 S33: -0.2300 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 52 B 139 REMARK 3 ORIGIN FOR THE GROUP (A): -27.6483 -27.9407 11.6846 REMARK 3 T TENSOR REMARK 3 T11: 0.1001 T22: 0.0895 REMARK 3 T33: 0.0506 T12: 0.0434 REMARK 3 T13: -0.0214 T23: 0.0443 REMARK 3 L TENSOR REMARK 3 L11: 10.2794 L22: 2.2380 REMARK 3 L33: 12.2976 L12: -4.3614 REMARK 3 L13: 10.9952 L23: -4.8347 REMARK 3 S TENSOR REMARK 3 S11: 0.5532 S12: -0.2945 S13: -0.4071 REMARK 3 S21: -0.3713 S22: 0.0047 S23: 0.1604 REMARK 3 S31: 0.6898 S32: -0.3482 S33: -0.5579 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 52 C 139 REMARK 3 ORIGIN FOR THE GROUP (A): -25.9688 -22.8609 12.6412 REMARK 3 T TENSOR REMARK 3 T11: 0.1546 T22: 0.2258 REMARK 3 T33: 0.1880 T12: 0.0831 REMARK 3 T13: -0.0632 T23: 0.0072 REMARK 3 L TENSOR REMARK 3 L11: 6.0110 L22: 2.3766 REMARK 3 L33: 6.8575 L12: -3.6583 REMARK 3 L13: 6.2289 L23: -3.9382 REMARK 3 S TENSOR REMARK 3 S11: -0.0227 S12: 0.3577 S13: 0.6335 REMARK 3 S21: -0.0851 S22: -0.3983 S23: -0.3099 REMARK 3 S31: 0.0740 S32: 0.4416 S33: 0.4211 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4ZDW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000208839. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-AUG-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.08090 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19416 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 85.440 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.900 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.10 REMARK 200 R MERGE FOR SHELL (I) : 0.51000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.800 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: 2EQB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 76.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE GROWN BY MIXING PROTEIN REMARK 280 COMPLEX WITH A RESERVOIR SOLUTION CONTAINING 24% PEG 3350, 0.2 M REMARK 280 SODIUM CITRATE IN A 1:1 RATIO AND WITH THE ADDITION OF 10MM GDP REMARK 280 TO THE DROP., VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 58.45000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 59.64000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 61.43000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 58.45000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 59.64000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 61.43000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 58.45000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 59.64000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 61.43000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 58.45000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 59.64000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 61.43000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: TRIMER ACCORDING TO GEL FILTRATION 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 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 18 REMARK 465 GLY A 66 REMARK 465 LYS A 67 REMARK 465 LYS A 68 REMARK 465 ASP B 141 REMARK 465 THR B 142 REMARK 465 ASP C 141 REMARK 465 THR C 142 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 105 CG CD OE1 OE2 REMARK 470 PHE A 108 CG CD1 CD2 CE1 CE2 CZ REMARK 470 SER B 50 OG REMARK 470 SER C 50 OG 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 GLN A 79 O HOH A 301 2.07 REMARK 500 OD1 ASP A 56 O HOH A 302 2.08 REMARK 500 O ASP C 103 OG SER C 107 2.16 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 TRP A 74 CE2 TRP A 74 CD2 0.074 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 GLN A 72 119.62 -162.46 REMARK 500 ASN A 110 3.55 -66.34 REMARK 500 ASP A 136 -96.66 -13.49 REMARK 500 GLU A 138 69.94 -116.16 REMARK 500 ASN A 168 8.44 56.17 REMARK 500 ILE A 172 -62.99 -23.21 REMARK 500 ASN B 51 -43.35 -130.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 135 ASP A 136 147.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP A 201 DBREF 4ZDW A 19 187 UNP P07560 SEC4_YEAST 19 187 DBREF 4ZDW B 51 142 UNP P17065 SEC2_YEAST 51 142 DBREF 4ZDW C 51 142 UNP P17065 SEC2_YEAST 51 142 SEQADV 4ZDW SER A 18 UNP P07560 EXPRESSION TAG SEQADV 4ZDW VAL A 29 UNP P07560 SER 29 ENGINEERED MUTATION SEQADV 4ZDW SER B 50 UNP P17065 EXPRESSION TAG SEQADV 4ZDW SER C 50 UNP P17065 EXPRESSION TAG SEQRES 1 A 170 SER SER ILE MET LYS ILE LEU LEU ILE GLY ASP VAL GLY SEQRES 2 A 170 VAL GLY LYS SER CYS LEU LEU VAL ARG PHE VAL GLU ASP SEQRES 3 A 170 LYS PHE ASN PRO SER PHE ILE THR THR ILE GLY ILE ASP SEQRES 4 A 170 PHE LYS ILE LYS THR VAL ASP ILE ASN GLY LYS LYS VAL SEQRES 5 A 170 LYS LEU GLN LEU TRP ASP THR ALA GLY GLN GLU ARG PHE SEQRES 6 A 170 ARG THR ILE THR THR ALA TYR TYR ARG GLY ALA MET GLY SEQRES 7 A 170 ILE ILE LEU VAL TYR ASP VAL THR ASP GLU ARG THR PHE SEQRES 8 A 170 THR ASN ILE LYS GLN TRP PHE LYS THR VAL ASN GLU HIS SEQRES 9 A 170 ALA ASN ASP GLU ALA GLN LEU LEU LEU VAL GLY ASN LYS SEQRES 10 A 170 SER ASP MET GLU THR ARG VAL VAL THR ALA ASP GLN GLY SEQRES 11 A 170 GLU ALA LEU ALA LYS GLU LEU GLY ILE PRO PHE ILE GLU SEQRES 12 A 170 SER SER ALA LYS ASN ASP ASP ASN VAL ASN GLU ILE PHE SEQRES 13 A 170 PHE THR LEU ALA LYS LEU ILE GLN GLU LYS ILE ASP SER SEQRES 14 A 170 ASN SEQRES 1 B 93 SER ASN TYR ASN GLN LEU LYS GLU ASP TYR ASN THR LEU SEQRES 2 B 93 LYS ARG GLU LEU SER ASP ARG ASP ASP GLU VAL LYS ARG SEQRES 3 B 93 LEU ARG GLU ASP ILE ALA LYS GLU ASN GLU LEU ARG THR SEQRES 4 B 93 LYS ALA GLU GLU GLU ALA ASP LYS LEU ASN LYS GLU VAL SEQRES 5 B 93 GLU ASP LEU THR ALA SER LEU PHE ASP GLU ALA ASN ASN SEQRES 6 B 93 MET VAL ALA ASP ALA ARG LYS GLU LYS TYR ALA ILE GLU SEQRES 7 B 93 ILE LEU ASN LYS ARG LEU THR GLU GLN LEU ARG GLU LYS SEQRES 8 B 93 ASP THR SEQRES 1 C 93 SER ASN TYR ASN GLN LEU LYS GLU ASP TYR ASN THR LEU SEQRES 2 C 93 LYS ARG GLU LEU SER ASP ARG ASP ASP GLU VAL LYS ARG SEQRES 3 C 93 LEU ARG GLU ASP ILE ALA LYS GLU ASN GLU LEU ARG THR SEQRES 4 C 93 LYS ALA GLU GLU GLU ALA ASP LYS LEU ASN LYS GLU VAL SEQRES 5 C 93 GLU ASP LEU THR ALA SER LEU PHE ASP GLU ALA ASN ASN SEQRES 6 C 93 MET VAL ALA ASP ALA ARG LYS GLU LYS TYR ALA ILE GLU SEQRES 7 C 93 ILE LEU ASN LYS ARG LEU THR GLU GLN LEU ARG GLU LYS SEQRES 8 C 93 ASP THR HET GDP A 201 28 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 4 GDP C10 H15 N5 O11 P2 FORMUL 5 HOH *16(H2 O) HELIX 1 AA1 LYS A 33 VAL A 41 1 9 HELIX 2 AA2 PHE A 82 ALA A 93 1 12 HELIX 3 AA3 ASP A 104 ASN A 110 1 7 HELIX 4 AA4 ASN A 110 ALA A 122 1 13 HELIX 5 AA5 THR A 143 GLY A 155 1 13 HELIX 6 AA6 ASN A 168 ASP A 185 1 18 HELIX 7 AA7 ASN B 51 GLU B 139 1 89 HELIX 8 AA8 ASN C 51 ARG C 138 1 88 SHEET 1 AA1 6 ILE A 55 LYS A 58 0 SHEET 2 AA1 6 LEU A 73 THR A 76 -1 O LEU A 73 N LYS A 58 SHEET 3 AA1 6 ILE A 23 ILE A 26 1 N ILE A 23 O TRP A 74 SHEET 4 AA1 6 GLY A 95 ASP A 101 1 O VAL A 99 N ILE A 26 SHEET 5 AA1 6 GLN A 127 ASN A 133 1 O ASN A 133 N TYR A 100 SHEET 6 AA1 6 GLU A 160 SER A 161 1 O SER A 161 N GLY A 132 CISPEP 1 SER B 50 ASN B 51 0 -9.06 SITE 1 AC1 16 ASP A 28 VAL A 29 GLY A 30 GLY A 32 SITE 2 AC1 16 LYS A 33 SER A 34 CYS A 35 ASN A 133 SITE 3 AC1 16 LYS A 134 ASP A 136 MET A 137 SER A 162 SITE 4 AC1 16 ALA A 163 LYS A 164 HOH A 303 HOH A 306 CRYST1 116.900 119.280 122.860 90.00 90.00 90.00 I 2 2 2 16 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 0.008554 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008384 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008139 0.00000