HEADER SIGNALING PROTEIN 08-AUG-22 8E0C TITLE CRYSTAL STRUCTURE OF HUMAN SAR1BH79G COMPND MOL_ID: 1; COMPND 2 MOLECULE: GTP-BINDING PROTEIN SAR1B; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GTP-BINDING PROTEIN B,GTBPB; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SAR1B, SARA2, SARB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SAR1B, GDP, COPII, SMALL GTPASE, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Q.HUANG REVDAT 2 28-FEB-24 8E0C 1 JRNL REVDAT 1 16-AUG-23 8E0C 0 JRNL AUTH Q.HUANG,D.M.E.SZEBENYI JRNL TITL THE ALARMONE PPGPP SELECTIVELY INHIBITS THE ISOFORM A OF THE JRNL TITL 2 HUMAN SMALL GTPASE SAR1. JRNL REF PROTEINS V. 91 518 2023 JRNL REFN ESSN 1097-0134 JRNL PMID 36369712 JRNL DOI 10.1002/PROT.26445 REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 12325 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1233 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 32.1480 - 4.1437 1.00 1334 149 0.1716 0.2159 REMARK 3 2 4.1437 - 3.2900 1.00 1267 140 0.1545 0.2285 REMARK 3 3 3.2900 - 2.8745 1.00 1247 139 0.1759 0.2399 REMARK 3 4 2.8745 - 2.6118 1.00 1234 137 0.1761 0.2301 REMARK 3 5 2.6118 - 2.4246 1.00 1227 137 0.1835 0.2498 REMARK 3 6 2.4246 - 2.2817 1.00 1213 134 0.1678 0.2385 REMARK 3 7 2.2817 - 2.1675 0.99 1212 135 0.1667 0.2559 REMARK 3 8 2.1675 - 2.0731 0.99 1198 134 0.1701 0.2328 REMARK 3 9 2.0731 - 1.9934 0.94 1160 128 0.1843 0.2803 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.670 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 1518 REMARK 3 ANGLE : 1.266 2056 REMARK 3 CHIRALITY : 0.050 231 REMARK 3 PLANARITY : 0.006 257 REMARK 3 DIHEDRAL : 14.516 560 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8E0C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1000267642. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9778 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12363 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.993 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.16400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.43800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 8DZM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2M (NH4)2SO4 AND 0.1M SODIUM REMARK 280 CITRATE, PH5.5., VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 20.32600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.70250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.26250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.70250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.32600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.26250 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 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 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 MET A 1 REMARK 465 SER A 2 REMARK 465 PHE A 3 REMARK 465 ILE A 4 REMARK 465 PHE A 5 REMARK 465 ASP A 6 REMARK 465 TRP A 7 REMARK 465 ILE A 8 REMARK 465 TYR A 9 REMARK 465 SER A 10 REMARK 465 GLY A 11 REMARK 465 PHE A 12 REMARK 465 SER A 13 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 OG1 THR A 39 O2G GTP A 201 2.05 REMARK 500 O HOH A 411 O HOH A 423 2.18 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 35 0.75 80.03 REMARK 500 PRO A 59 -89.67 -10.77 REMARK 500 ALA A 67 -119.40 51.70 REMARK 500 ASP A 104 79.50 -106.75 REMARK 500 LYS A 166 -158.71 -125.03 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 A 203 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 62 OE2 REMARK 620 2 GTP A 201 O1G 101.2 REMARK 620 3 GTP A 201 O2G 105.3 56.4 REMARK 620 N 1 2 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 GTP A 201 O2G REMARK 620 2 GTP A 201 O3B 55.2 REMARK 620 3 GTP A 201 O1A 131.1 76.4 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8E0A RELATED DB: PDB REMARK 900 MUTANT DBREF 8E0C A 1 198 UNP Q9Y6B6 SAR1B_HUMAN 1 198 SEQADV 8E0C GLY A 79 UNP Q9Y6B6 HIS 79 ENGINEERED MUTATION SEQRES 1 A 198 MET SER PHE ILE PHE ASP TRP ILE TYR SER GLY PHE SER SEQRES 2 A 198 SER VAL LEU GLN PHE LEU GLY LEU TYR LYS LYS THR GLY SEQRES 3 A 198 LYS LEU VAL PHE LEU GLY LEU ASP ASN ALA GLY LYS THR SEQRES 4 A 198 THR LEU LEU HIS MET LEU LYS ASP ASP ARG LEU GLY GLN SEQRES 5 A 198 HIS VAL PRO THR LEU HIS PRO THR SER GLU GLU LEU THR SEQRES 6 A 198 ILE ALA GLY MET THR PHE THR THR PHE ASP LEU GLY GLY SEQRES 7 A 198 GLY VAL GLN ALA ARG ARG VAL TRP LYS ASN TYR LEU PRO SEQRES 8 A 198 ALA ILE ASN GLY ILE VAL PHE LEU VAL ASP CYS ALA ASP SEQRES 9 A 198 HIS GLU ARG LEU LEU GLU SER LYS GLU GLU LEU ASP SER SEQRES 10 A 198 LEU MET THR ASP GLU THR ILE ALA ASN VAL PRO ILE LEU SEQRES 11 A 198 ILE LEU GLY ASN LYS ILE ASP ARG PRO GLU ALA ILE SER SEQRES 12 A 198 GLU GLU ARG LEU ARG GLU MET PHE GLY LEU TYR GLY GLN SEQRES 13 A 198 THR THR GLY LYS GLY SER ILE SER LEU LYS GLU LEU ASN SEQRES 14 A 198 ALA ARG PRO LEU GLU VAL PHE MET CYS SER VAL LEU LYS SEQRES 15 A 198 ARG GLN GLY TYR GLY GLU GLY PHE ARG TRP MET ALA GLN SEQRES 16 A 198 TYR ILE ASP HET GTP A 201 32 HET MG A 202 1 HET MG A 203 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 GTP C10 H16 N5 O14 P3 FORMUL 3 MG 2(MG 2+) FORMUL 5 HOH *129(H2 O) HELIX 1 AA1 SER A 14 GLY A 20 1 7 HELIX 2 AA2 GLY A 37 LYS A 46 1 10 HELIX 3 AA3 VAL A 80 LEU A 90 1 11 HELIX 4 AA4 ASP A 104 GLU A 106 5 3 HELIX 5 AA5 ARG A 107 THR A 120 1 14 HELIX 6 AA6 ASP A 121 ALA A 125 5 5 HELIX 7 AA7 SER A 143 PHE A 151 1 9 HELIX 8 AA8 GLY A 185 GLN A 195 1 11 SHEET 1 AA1 7 THR A 56 HIS A 58 0 SHEET 2 AA1 7 SER A 61 ILE A 66 -1 O SER A 61 N HIS A 58 SHEET 3 AA1 7 MET A 69 THR A 73 -1 O PHE A 71 N LEU A 64 SHEET 4 AA1 7 GLY A 26 LEU A 31 1 N LEU A 28 O THR A 70 SHEET 5 AA1 7 GLY A 95 ASP A 101 1 O VAL A 97 N LEU A 31 SHEET 6 AA1 7 ILE A 129 ASN A 134 1 O LEU A 130 N ILE A 96 SHEET 7 AA1 7 LEU A 173 MET A 177 1 O GLU A 174 N ILE A 131 LINK OE2 GLU A 62 MG MG A 203 1555 1555 2.53 LINK O2G GTP A 201 MG MG A 202 1555 1555 1.94 LINK O3B GTP A 201 MG MG A 202 1555 1555 2.99 LINK O1A GTP A 201 MG MG A 202 1555 1555 2.49 LINK O1G GTP A 201 MG MG A 203 1555 1555 2.91 LINK O2G GTP A 201 MG MG A 203 1555 1555 1.85 CRYST1 40.652 52.525 81.405 90.00 90.00 90.00 P 21 21 21 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 0.024599 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019039 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012284 0.00000