HEADER GTP BINDING PROTEIN 09-APR-15 4Z8Y TITLE CRYSTAL STRUCTURE OF RAB GTPASE SEC4P MUTANT - S29V COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN SEC4; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SUPPRESSOR OF RHO3 PROTEIN 6; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: 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 KEYWDS GTPASE, GDP BOUND, RAB, GTP BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.C.RINADI,R.N.COLLINS REVDAT 2 27-SEP-23 4Z8Y 1 REMARK LINK REVDAT 1 14-OCT-15 4Z8Y 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. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 3 NUMBER OF REFLECTIONS : 21712 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.239 REMARK 3 R VALUE (WORKING SET) : 0.236 REMARK 3 FREE R VALUE : 0.298 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1170 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1575 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.33 REMARK 3 BIN R VALUE (WORKING SET) : 0.5540 REMARK 3 BIN FREE R VALUE SET COUNT : 76 REMARK 3 BIN FREE R VALUE : 0.5370 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2591 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 61 REMARK 3 SOLVENT ATOMS : 345 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.03000 REMARK 3 B22 (A**2) : 0.04000 REMARK 3 B33 (A**2) : -0.01000 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): 0.259 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.220 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.154 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.456 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.912 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.872 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2687 ; 0.011 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3635 ; 1.610 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 324 ; 6.493 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 119 ;39.189 ;25.378 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 499 ;18.878 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;16.805 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 425 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1933 ; 0.006 ; 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 : NULL 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: NULL REMARK 4 REMARK 4 4Z8Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000208163. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23244 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.870 REMARK 200 RESOLUTION RANGE LOW (A) : 66.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : 1.700 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : 0.05200 REMARK 200 FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 1.60 REMARK 200 R MERGE FOR SHELL (I) : 0.28500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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: 1G16 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AFTER INITIAL CRYSTAL SCREENING, SMALL REMARK 280 CRYSTALS WERE OBTAINED IN 14% PEG3350, 200MM ZINC ACETATE. AFTER REMARK 280 REFINEMENT, LARGE SINGLE CRYSTALS WERE OBTAINED IN 14% PEG4000, REMARK 280 50MM ZINC ACETATE., BATCH MODE, TEMPERATURE 293.15K 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 37.72500 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 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 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 18 REMARK 465 SER A 48 REMARK 465 PHE A 49 REMARK 465 ILE A 50 REMARK 465 THR A 51 REMARK 465 THR A 52 REMARK 465 ILE A 53 REMARK 465 ASP A 185 REMARK 465 SER A 186 REMARK 465 ASN A 187 REMARK 465 SER B 18 REMARK 465 SER B 186 REMARK 465 ASN B 187 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 GLN A 79 CG CD OE1 NE2 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 OD2 ASP B 185 O HOH B 301 1.86 REMARK 500 OE1 GLU A 120 O HOH A 301 1.88 REMARK 500 O ILE A 85 O HOH A 302 1.91 REMARK 500 O HOH B 344 O HOH B 350 1.98 REMARK 500 N SER A 19 O HOH A 303 2.05 REMARK 500 O HOH A 308 O HOH A 411 2.09 REMARK 500 OD1 ASP A 124 O HOH A 304 2.11 REMARK 500 O HOH B 311 O HOH B 325 2.14 REMARK 500 CD2 PHE B 173 O HOH B 307 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 CZ PHE A 82 O HOH A 336 1455 1.91 REMARK 500 O HOH A 352 O HOH B 424 1655 1.94 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 A 46 -75.79 -111.95 REMARK 500 THR A 84 -19.58 -48.54 REMARK 500 LYS A 134 34.70 73.18 REMARK 500 ASP B 56 -60.88 -98.39 REMARK 500 ARG B 81 -120.88 45.79 REMARK 500 LYS B 134 30.49 71.94 REMARK 500 ILE B 184 89.64 -68.39 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 A 481 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH B 463 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH B 464 DISTANCE = 6.34 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 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 34 OG REMARK 620 2 GDP A 201 O3B 85.5 REMARK 620 3 HOH A 314 O 83.4 92.8 REMARK 620 4 HOH A 318 O 174.9 92.9 91.8 REMARK 620 5 HOH A 380 O 97.6 94.6 172.6 87.4 REMARK 620 6 HOH A 422 O 92.1 170.6 77.9 88.7 94.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 43 OD1 REMARK 620 2 ASP A 43 OD2 54.5 REMARK 620 3 ASP A 166 OD2 107.3 159.0 REMARK 620 4 HOH A 404 O 110.8 92.0 105.6 REMARK 620 5 HIS B 121 NE2 81.1 98.7 87.3 42.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 121 NE2 REMARK 620 2 HOH A 302 O 92.6 REMARK 620 3 ASP B 43 OD1 160.2 81.6 REMARK 620 4 ASP B 43 OD2 100.1 84.8 60.6 REMARK 620 5 ASP B 166 OD2 101.0 88.1 97.8 158.0 REMARK 620 6 HOH B 366 O 94.6 172.7 91.2 92.8 91.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 34 OG REMARK 620 2 GDP B 201 O2B 91.1 REMARK 620 3 HOH B 323 O 87.7 91.7 REMARK 620 4 HOH B 356 O 91.4 90.7 177.4 REMARK 620 5 HOH B 382 O 171.4 97.4 92.9 87.5 REMARK 620 6 HOH B 391 O 91.4 173.8 82.7 94.9 80.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 204 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 56 OD2 REMARK 620 2 GLU B 182 OE1 74.0 REMARK 620 N 1 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 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 204 DBREF 4Z8Y A 19 187 UNP P07560 SEC4_YEAST 19 187 DBREF 4Z8Y B 19 187 UNP P07560 SEC4_YEAST 19 187 SEQADV 4Z8Y SER A 18 UNP P07560 EXPRESSION TAG SEQADV 4Z8Y VAL A 29 UNP P07560 SER 29 ENGINEERED MUTATION SEQADV 4Z8Y SER B 18 UNP P07560 EXPRESSION TAG SEQADV 4Z8Y VAL B 29 UNP P07560 SER 29 ENGINEERED MUTATION 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 170 SER SER ILE MET LYS ILE LEU LEU ILE GLY ASP VAL GLY SEQRES 2 B 170 VAL GLY LYS SER CYS LEU LEU VAL ARG PHE VAL GLU ASP SEQRES 3 B 170 LYS PHE ASN PRO SER PHE ILE THR THR ILE GLY ILE ASP SEQRES 4 B 170 PHE LYS ILE LYS THR VAL ASP ILE ASN GLY LYS LYS VAL SEQRES 5 B 170 LYS LEU GLN LEU TRP ASP THR ALA GLY GLN GLU ARG PHE SEQRES 6 B 170 ARG THR ILE THR THR ALA TYR TYR ARG GLY ALA MET GLY SEQRES 7 B 170 ILE ILE LEU VAL TYR ASP VAL THR ASP GLU ARG THR PHE SEQRES 8 B 170 THR ASN ILE LYS GLN TRP PHE LYS THR VAL ASN GLU HIS SEQRES 9 B 170 ALA ASN ASP GLU ALA GLN LEU LEU LEU VAL GLY ASN LYS SEQRES 10 B 170 SER ASP MET GLU THR ARG VAL VAL THR ALA ASP GLN GLY SEQRES 11 B 170 GLU ALA LEU ALA LYS GLU LEU GLY ILE PRO PHE ILE GLU SEQRES 12 B 170 SER SER ALA LYS ASN ASP ASP ASN VAL ASN GLU ILE PHE SEQRES 13 B 170 PHE THR LEU ALA LYS LEU ILE GLN GLU LYS ILE ASP SER SEQRES 14 B 170 ASN HET GDP A 201 28 HET MG A 202 1 HET ZN A 203 1 HET GDP B 201 28 HET MG B 202 1 HET ZN B 203 1 HET ZN B 204 1 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM ZN ZINC ION FORMUL 3 GDP 2(C10 H15 N5 O11 P2) FORMUL 4 MG 2(MG 2+) FORMUL 5 ZN 3(ZN 2+) FORMUL 10 HOH *345(H2 O) HELIX 1 AA1 GLY A 32 ASP A 43 1 12 HELIX 2 AA2 PHE A 82 THR A 86 5 5 HELIX 3 AA3 THR A 87 ARG A 91 5 5 HELIX 4 AA4 ASP A 104 ASN A 110 1 7 HELIX 5 AA5 ASN A 110 ALA A 122 1 13 HELIX 6 AA6 THR A 143 GLY A 155 1 13 HELIX 7 AA7 ASN A 168 ILE A 184 1 17 HELIX 8 AA8 GLY B 32 ASP B 43 1 12 HELIX 9 AA9 SER B 48 ILE B 53 1 6 HELIX 10 AB1 THR B 86 ARG B 91 1 6 HELIX 11 AB2 ASP B 104 ASN B 110 1 7 HELIX 12 AB3 ASN B 110 ALA B 122 1 13 HELIX 13 AB4 THR B 143 GLY B 155 1 13 HELIX 14 AB5 ASN B 168 ILE B 184 1 17 SHEET 1 AA1 6 PHE A 57 ILE A 64 0 SHEET 2 AA1 6 LYS A 67 TRP A 74 -1 O VAL A 69 N VAL A 62 SHEET 3 AA1 6 ILE A 20 ILE A 26 1 N ILE A 23 O TRP A 74 SHEET 4 AA1 6 ALA A 93 ASP A 101 1 O ILE A 97 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 PHE A 158 GLU A 160 1 O ILE A 159 N LEU A 130 SHEET 1 AA2 6 PHE B 57 ILE B 64 0 SHEET 2 AA2 6 LYS B 67 ASP B 75 -1 O VAL B 69 N VAL B 62 SHEET 3 AA2 6 ILE B 20 GLY B 27 1 N ILE B 23 O TRP B 74 SHEET 4 AA2 6 ALA B 93 ASP B 101 1 O ILE B 97 N LEU B 24 SHEET 5 AA2 6 GLN B 127 ASN B 133 1 O ASN B 133 N TYR B 100 SHEET 6 AA2 6 PHE B 158 GLU B 160 1 O ILE B 159 N GLY B 132 LINK OG SER A 34 MG MG A 202 1555 1555 1.93 LINK OD1 ASP A 43 ZN ZN A 203 1555 1555 2.01 LINK OD2 ASP A 43 ZN ZN A 203 1555 1555 2.63 LINK NE2 HIS A 121 ZN ZN B 203 1555 1555 2.11 LINK OD2 ASP A 166 ZN ZN A 203 1555 1555 1.85 LINK O3B GDP A 201 MG MG A 202 1555 1555 2.03 LINK MG MG A 202 O HOH A 314 1555 1555 1.77 LINK MG MG A 202 O HOH A 318 1555 1555 2.02 LINK MG MG A 202 O HOH A 380 1555 1555 1.81 LINK MG MG A 202 O HOH A 422 1555 1555 2.33 LINK ZN ZN A 203 O HOH A 404 1555 1555 2.08 LINK ZN ZN A 203 NE2 HIS B 121 1454 1555 1.97 LINK O HOH A 302 ZN ZN B 203 1555 1555 2.08 LINK OG SER B 34 MG MG B 202 1555 1555 1.99 LINK OD1 ASP B 43 ZN ZN B 203 1555 1555 2.24 LINK OD2 ASP B 43 ZN ZN B 203 1555 1555 2.12 LINK OD2 ASP B 56 ZN ZN B 204 1555 1455 2.32 LINK OD2 ASP B 166 ZN ZN B 203 1555 1555 1.93 LINK OE1 GLU B 182 ZN ZN B 204 1555 1555 2.03 LINK O2B GDP B 201 MG MG B 202 1555 1555 1.95 LINK MG MG B 202 O HOH B 323 1555 1555 1.80 LINK MG MG B 202 O HOH B 356 1555 1555 1.97 LINK MG MG B 202 O HOH B 382 1555 1555 1.93 LINK MG MG B 202 O HOH B 391 1555 1555 2.08 LINK ZN ZN B 203 O HOH B 366 1555 1555 1.99 SITE 1 AC1 23 VAL A 29 GLY A 30 VAL A 31 GLY A 32 SITE 2 AC1 23 LYS A 33 SER A 34 CYS A 35 PHE A 45 SITE 3 AC1 23 PRO A 47 ASN A 133 LYS A 134 ASP A 136 SITE 4 AC1 23 MET A 137 SER A 162 ALA A 163 LYS A 164 SITE 5 AC1 23 MG A 202 HOH A 314 HOH A 318 HOH A 360 SITE 6 AC1 23 HOH A 374 HOH A 380 HOH A 401 SITE 1 AC2 6 SER A 34 GDP A 201 HOH A 314 HOH A 318 SITE 2 AC2 6 HOH A 380 HOH A 422 SITE 1 AC3 5 ASP A 43 ASP A 166 HOH A 404 ILE B 85 SITE 2 AC3 5 HIS B 121 SITE 1 AC4 22 VAL B 29 GLY B 30 VAL B 31 GLY B 32 SITE 2 AC4 22 LYS B 33 SER B 34 CYS B 35 PRO B 47 SITE 3 AC4 22 ASN B 133 LYS B 134 ASP B 136 MET B 137 SITE 4 AC4 22 SER B 162 ALA B 163 LYS B 164 MG B 202 SITE 5 AC4 22 HOH B 310 HOH B 318 HOH B 323 HOH B 356 SITE 6 AC4 22 HOH B 382 HOH B 397 SITE 1 AC5 6 SER B 34 GDP B 201 HOH B 323 HOH B 356 SITE 2 AC5 6 HOH B 382 HOH B 391 SITE 1 AC6 6 ILE A 85 HIS A 121 HOH A 302 ASP B 43 SITE 2 AC6 6 ASP B 166 HOH B 366 SITE 1 AC7 4 ASP B 56 GLU B 182 HOH B 344 HOH B 444 CRYST1 31.720 75.450 66.230 90.00 91.58 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 0.031526 0.000000 0.000870 0.00000 SCALE2 0.000000 0.013254 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015105 0.00000