HEADER PROTEIN TRANSPORT 07-APR-23 8SDW TITLE CRYSTAL STRUCTURE OF THE NON-MYRISTOYLATED MUTANT [L8K]ARF1 IN COMPLEX TITLE 2 WITH A GDP ANALOGUE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADP-RIBOSYLATION FACTOR 1; COMPND 3 CHAIN: A; COMPND 4 EC: 3.6.5.2; 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: ARF1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL-21(DE3) KEYWDS GTPASE, G PROTEIN, GDP, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR E.M.ROSENBERG JR.,P.A.RANDAZZO,L.ESSER,D.XIA REVDAT 2 24-APR-24 8SDW 1 JRNL REVDAT 1 28-JUN-23 8SDW 0 JRNL AUTH E.M.ROSENBERG JR.,X.JIAN,O.SOUBIAS,R.A.JACKSON,E.GLADU, JRNL AUTH 2 E.ANDERSEN,L.ESSER,A.J.SODT,D.XIA,R.A.BYRD,P.A.RANDAZZO JRNL TITL POINT MUTATIONS IN ARF1 REVEAL COOPERATIVE EFFECTS OF THE JRNL TITL 2 N-TERMINAL EXTENSION AND MYRISTATE FOR GTPASE-ACTIVATING JRNL TITL 3 PROTEIN CATALYTIC ACTIVITY. JRNL REF PLOS ONE V. 19 95103 2024 JRNL REFN ESSN 1932-6203 JRNL PMID 38574162 JRNL DOI 10.1371/JOURNAL.PONE.0295103 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20RC3-4406 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 18573 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 1.8100 - 1.7500 0.00 0 1852 0.2151 0.2323 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 8SDW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-APR-23. REMARK 100 THE DEPOSITION ID IS D_1000273577. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18613 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 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 (%) : 98.7 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NEEDLE-LIKE CRYSTALS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM NITRATE, 20% W/V REMARK 280 POLYETHYLENE GLYCOL 3,350, PH 6.8, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277.15K 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 20.82700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.23600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.50750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.23600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.82700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.50750 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 GLY A 2 REMARK 465 ASN A 3 REMARK 465 ILE A 4 REMARK 465 PHE A 5 REMARK 465 GLY A 70 REMARK 465 GLN A 71 REMARK 465 ASP A 72 REMARK 465 LYS A 73 REMARK 465 ILE A 74 REMARK 465 LYS A 181 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 LYS A 38 CE NZ REMARK 470 ARG A 75 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 77 CG CD1 CD2 REMARK 470 ARG A 79 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 80 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 109 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 117 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 149 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 150 CG ND1 CD2 CE1 NE2 REMARK 470 GLN A 180 CG CD OE1 NE2 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 LYS A 59 -113.97 48.77 REMARK 500 LYS A 127 35.41 70.42 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 596 DISTANCE = 6.53 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 THR A 31 OG1 REMARK 620 2 G3D A 201 O2B 85.0 REMARK 620 3 HOH A 334 O 176.6 95.5 REMARK 620 4 HOH A 341 O 88.4 86.1 88.3 REMARK 620 5 HOH A 453 O 91.8 92.7 91.5 178.8 REMARK 620 6 HOH A 471 O 90.4 172.6 88.9 88.0 93.2 REMARK 620 N 1 2 3 4 5 DBREF 8SDW A 1 181 UNP P84077 ARF1_HUMAN 1 181 SEQADV 8SDW LYS A 8 UNP P84077 LEU 8 ENGINEERED MUTATION SEQRES 1 A 181 MET GLY ASN ILE PHE ALA ASN LYS PHE LYS GLY LEU PHE SEQRES 2 A 181 GLY LYS LYS GLU MET ARG ILE LEU MET VAL GLY LEU ASP SEQRES 3 A 181 ALA ALA GLY LYS THR THR ILE LEU TYR LYS LEU LYS LEU SEQRES 4 A 181 GLY GLU ILE VAL THR THR ILE PRO THR ILE GLY PHE ASN SEQRES 5 A 181 VAL GLU THR VAL GLU TYR LYS ASN ILE SER PHE THR VAL SEQRES 6 A 181 TRP ASP VAL GLY GLY GLN ASP LYS ILE ARG PRO LEU TRP SEQRES 7 A 181 ARG HIS TYR PHE GLN ASN THR GLN GLY LEU ILE PHE VAL SEQRES 8 A 181 VAL ASP SER ASN ASP ARG GLU ARG VAL ASN GLU ALA ARG SEQRES 9 A 181 GLU GLU LEU MET ARG MET LEU ALA GLU ASP GLU LEU ARG SEQRES 10 A 181 ASP ALA VAL LEU LEU VAL PHE ALA ASN LYS GLN ASP LEU SEQRES 11 A 181 PRO ASN ALA MET ASN ALA ALA GLU ILE THR ASP LYS LEU SEQRES 12 A 181 GLY LEU HIS SER LEU ARG HIS ARG ASN TRP TYR ILE GLN SEQRES 13 A 181 ALA THR CYS ALA THR SER GLY ASP GLY LEU TYR GLU GLY SEQRES 14 A 181 LEU ASP TRP LEU SER ASN GLN LEU ARG ASN GLN LYS HET G3D A 201 32 HET MG A 202 1 HETNAM G3D GUANOSINE-3'-MONOPHOSPHATE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 G3D C10 H16 N5 O14 P3 FORMUL 3 MG MG 2+ FORMUL 4 HOH *296(H2 O) HELIX 1 AA1 GLY A 29 LYS A 38 1 10 HELIX 2 AA2 PRO A 76 ASN A 84 1 9 HELIX 3 AA3 ASP A 96 GLU A 98 5 3 HELIX 4 AA4 ARG A 99 ALA A 112 1 14 HELIX 5 AA5 GLU A 113 ARG A 117 5 5 HELIX 6 AA6 ASN A 135 GLY A 144 1 10 HELIX 7 AA7 LEU A 145 LEU A 148 5 4 HELIX 8 AA8 GLY A 165 ASN A 179 1 15 SHEET 1 AA1 7 VAL A 43 THR A 48 0 SHEET 2 AA1 7 PHE A 51 TYR A 58 -1 O VAL A 53 N THR A 45 SHEET 3 AA1 7 ILE A 61 ASP A 67 -1 O PHE A 63 N VAL A 56 SHEET 4 AA1 7 MET A 18 GLY A 24 1 N MET A 22 O THR A 64 SHEET 5 AA1 7 GLY A 87 ASP A 93 1 O ILE A 89 N LEU A 21 SHEET 6 AA1 7 VAL A 120 ASN A 126 1 O VAL A 120 N LEU A 88 SHEET 7 AA1 7 TRP A 153 ALA A 157 1 O GLN A 156 N VAL A 123 LINK OG1 THR A 31 MG MG A 202 1555 1555 2.16 LINK O2B G3D A 201 MG MG A 202 1555 1555 2.16 LINK MG MG A 202 O HOH A 334 1555 1555 2.10 LINK MG MG A 202 O HOH A 341 1555 1555 2.23 LINK MG MG A 202 O HOH A 453 1555 1555 2.04 LINK MG MG A 202 O HOH A 471 1555 1555 2.10 CRYST1 41.654 55.015 78.472 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 0.024007 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018177 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012743 0.00000