HEADER HYDROLASE 29-FEB-24 8YIM TITLE CRYSTAL STRUCTURE OF HUMAN RAB23 IN COMPLEX WITH GMPPNP (1.35 TITLE 2 ANGSTROMS RESOLUTION) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN RAB-23; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: TRUNCATED TO RESIDUES 7-172 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RAB23, HSPC137; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SMALL GTPASE ROSSMANN FOLD, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.Y.CHAU,H.LIANG,W.S.AIK REVDAT 3 08-JAN-25 8YIM 1 JRNL REVDAT 2 18-DEC-24 8YIM 1 JRNL REVDAT 1 04-DEC-24 8YIM 0 JRNL AUTH Y.Y.CHAU,H.LIANG,W.L.TUNG,C.H.H.HOR,W.S.AIK JRNL TITL STRUCTURAL BASIS FOR RAB23 ACTIVATION AND A LOSS-OF-FUNCTION JRNL TITL 2 MUTATION IN CARPENTER SYNDROME. JRNL REF J.BIOL.CHEM. V. 301 08036 2024 JRNL REFN ESSN 1083-351X JRNL PMID 39615683 JRNL DOI 10.1016/J.JBC.2024.108036 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 44369 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.151 REMARK 3 R VALUE (WORKING SET) : 0.150 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.310 REMARK 3 FREE R VALUE TEST SET COUNT : 2354 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 22.8800 - 3.4700 1.00 2618 189 0.1592 0.1753 REMARK 3 2 3.4700 - 2.7500 1.00 2523 140 0.1653 0.1820 REMARK 3 3 2.7500 - 2.4100 1.00 2487 165 0.1640 0.1947 REMARK 3 4 2.4100 - 2.1900 1.00 2490 122 0.1477 0.1684 REMARK 3 5 2.1900 - 2.0300 1.00 2468 141 0.1375 0.1625 REMARK 3 6 2.0300 - 1.9100 1.00 2500 132 0.1353 0.1637 REMARK 3 7 1.9100 - 1.8100 1.00 2447 146 0.1391 0.1693 REMARK 3 8 1.8100 - 1.7400 1.00 2459 123 0.1350 0.1784 REMARK 3 9 1.7400 - 1.6700 1.00 2453 144 0.1275 0.1825 REMARK 3 10 1.6700 - 1.6100 1.00 2492 118 0.1281 0.1611 REMARK 3 11 1.6100 - 1.5600 1.00 2417 141 0.1266 0.1727 REMARK 3 12 1.5600 - 1.5200 1.00 2476 95 0.1300 0.1625 REMARK 3 13 1.5200 - 1.4800 1.00 2451 123 0.1346 0.2045 REMARK 3 14 1.4800 - 1.4400 1.00 2438 130 0.1423 0.2009 REMARK 3 15 1.4400 - 1.4100 1.00 2434 132 0.1567 0.2009 REMARK 3 16 1.4100 - 1.3800 1.00 2424 152 0.1743 0.1961 REMARK 3 17 1.3800 - 1.3500 1.00 2438 161 0.1898 0.2348 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) : 0.111 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.525 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.58 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 : 0.003 1348 REMARK 3 ANGLE : 0.681 1831 REMARK 3 CHIRALITY : 0.065 212 REMARK 3 PLANARITY : 0.003 229 REMARK 3 DIHEDRAL : 14.210 516 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 8YIM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-MAR-24. REMARK 100 THE DEPOSITION ID IS D_1300045601. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 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 FR-X 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : RIGAKU HYPIX-6000HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : CRYSALISPRO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44414 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 22.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.000 REMARK 200 R MERGE (I) : 0.13300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 2.08700 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: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M IMIDAZOLE PH 8.0, 0.2M NACL, 0.4M REMARK 280 SODIUM PHOSPHATE MONOBASIC/1.6M POTASSIUM PHOSPHATE DIBASIC, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.30667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 62.61333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 62.61333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 31.30667 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 TOTAL BURIED SURFACE AREA: 1010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 486 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 492 LIES ON A SPECIAL POSITION. 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 6 REMARK 465 GLU A 69 REMARK 465 GLU A 70 REMARK 465 PHE A 71 REMARK 465 ASP A 72 REMARK 465 ALA A 73 REMARK 465 LYS A 172 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 31 CD CE NZ REMARK 470 LYS A 39 CD CE NZ REMARK 470 GLN A 50 CG CD OE1 NE2 REMARK 470 ASN A 54 CG OD1 ND2 REMARK 470 ASP A 55 CG OD1 OD2 REMARK 470 GLU A 56 CG CD OE1 OE2 REMARK 470 GLN A 68 CG CD OE1 NE2 REMARK 470 GLU A 95 CD OE1 OE2 REMARK 470 ASP A 113 CG OD1 OD2 REMARK 470 LEU A 126 CG CD1 CD2 REMARK 470 ASP A 127 CG OD1 OD2 REMARK 470 GLN A 171 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 ASN A 54 -121.96 54.65 REMARK 500 ASP A 55 63.98 -112.73 REMARK 500 LEU A 125 35.01 -94.39 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 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 23 OG REMARK 620 2 THR A 41 OG1 78.2 REMARK 620 3 GNP A 201 O1G 172.5 94.9 REMARK 620 4 GNP A 201 O2B 90.4 168.4 96.6 REMARK 620 5 HOH A 315 O 89.2 90.4 93.7 87.5 REMARK 620 6 HOH A 331 O 85.2 91.2 92.1 89.8 173.8 REMARK 620 N 1 2 3 4 5 DBREF 8YIM A 7 172 UNP Q9ULC3 RAB23_HUMAN 7 172 SEQADV 8YIM SER A 6 UNP Q9ULC3 EXPRESSION TAG SEQRES 1 A 167 SER GLU VAL ALA ILE LYS MET VAL VAL VAL GLY ASN GLY SEQRES 2 A 167 ALA VAL GLY LYS SER SER MET ILE GLN ARG TYR CYS LYS SEQRES 3 A 167 GLY ILE PHE THR LYS ASP TYR LYS LYS THR ILE GLY VAL SEQRES 4 A 167 ASP PHE LEU GLU ARG GLN ILE GLN VAL ASN ASP GLU ASP SEQRES 5 A 167 VAL ARG LEU MET LEU TRP ASP THR ALA GLY GLN GLU GLU SEQRES 6 A 167 PHE ASP ALA ILE THR LYS ALA TYR TYR ARG GLY ALA GLN SEQRES 7 A 167 ALA CYS VAL LEU VAL PHE SER THR THR ASP ARG GLU SER SEQRES 8 A 167 PHE GLU ALA VAL SER SER TRP ARG GLU LYS VAL VAL ALA SEQRES 9 A 167 GLU VAL GLY ASP ILE PRO THR VAL LEU VAL GLN ASN LYS SEQRES 10 A 167 ILE ASP LEU LEU ASP ASP SER CYS ILE LYS ASN GLU GLU SEQRES 11 A 167 ALA GLU ALA LEU ALA LYS ARG LEU LYS LEU ARG PHE TYR SEQRES 12 A 167 ARG THR SER VAL LYS GLU ASP LEU ASN VAL ASN GLU VAL SEQRES 13 A 167 PHE LYS TYR LEU ALA GLU LYS TYR LEU GLN LYS HET GNP A 201 32 HET MG A 202 1 HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER HETNAM MG MAGNESIUM ION FORMUL 2 GNP C10 H17 N6 O13 P3 FORMUL 3 MG MG 2+ FORMUL 4 HOH *193(H2 O) HELIX 1 AA1 GLY A 21 GLY A 32 1 12 HELIX 2 AA2 THR A 75 ARG A 80 1 6 HELIX 3 AA3 ASP A 93 ALA A 99 1 7 HELIX 4 AA4 ALA A 99 GLY A 112 1 14 HELIX 5 AA5 LYS A 122 SER A 129 5 8 HELIX 6 AA6 LYS A 132 LYS A 144 1 13 HELIX 7 AA7 ASN A 157 GLN A 171 1 15 SHEET 1 AA1 6 VAL A 44 GLN A 52 0 SHEET 2 AA1 6 ASP A 57 THR A 65 -1 O LEU A 60 N ARG A 49 SHEET 3 AA1 6 VAL A 8 VAL A 15 1 N ILE A 10 O MET A 61 SHEET 4 AA1 6 ALA A 84 SER A 90 1 O VAL A 88 N VAL A 15 SHEET 5 AA1 6 THR A 116 ASN A 121 1 O VAL A 119 N LEU A 87 SHEET 6 AA1 6 ARG A 146 ARG A 149 1 O ARG A 146 N LEU A 118 LINK OG SER A 23 MG MG A 202 1555 1555 2.06 LINK OG1 THR A 41 MG MG A 202 1555 1555 2.04 LINK O1G GNP A 201 MG MG A 202 1555 1555 2.06 LINK O2B GNP A 201 MG MG A 202 1555 1555 2.12 LINK MG MG A 202 O HOH A 315 1555 1555 2.11 LINK MG MG A 202 O HOH A 331 1555 1555 2.10 CRYST1 60.523 60.523 93.920 90.00 90.00 120.00 P 31 2 1 6 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 0.016523 0.009539 0.000000 0.00000 SCALE2 0.000000 0.019079 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010647 0.00000