HEADER HYDROLASE 12-MAR-24 8YO0 TITLE CRYSTAL STRUCTURE OF HUMAN RAB23 Y79DEL IN COMPLEX WITH GDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN RAB-23; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 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: RAB23, HSPC137; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SMALL GTPASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.LIANG,Y.Y.CHAU,W.S.AIK REVDAT 2 18-DEC-24 8YO0 1 JRNL REVDAT 1 04-DEC-24 8YO0 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. 08036 2024 JRNL REFN ESSN 1083-351X JRNL PMID 39615683 JRNL DOI 10.1016/J.JBC.2024.108036 REMARK 2 REMARK 2 RESOLUTION. 1.30 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 39421 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1971 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 15.6400 - 3.1300 0.99 2817 148 0.1680 0.1877 REMARK 3 2 3.1300 - 2.4800 1.00 2739 144 0.1656 0.1828 REMARK 3 3 2.4800 - 2.1700 1.00 2698 143 0.1395 0.1642 REMARK 3 4 2.1700 - 1.9700 1.00 2689 141 0.1299 0.1563 REMARK 3 5 1.9700 - 1.8300 1.00 2678 141 0.1390 0.1631 REMARK 3 6 1.8300 - 1.7200 1.00 2661 140 0.1393 0.1839 REMARK 3 7 1.7200 - 1.6400 1.00 2656 140 0.1351 0.1958 REMARK 3 8 1.6400 - 1.5700 1.00 2650 139 0.1445 0.1690 REMARK 3 9 1.5700 - 1.5100 1.00 2647 139 0.1465 0.1842 REMARK 3 10 1.5100 - 1.4500 1.00 2647 140 0.1657 0.2055 REMARK 3 11 1.4500 - 1.4100 1.00 2646 139 0.1844 0.2152 REMARK 3 12 1.4100 - 1.3700 1.00 2616 138 0.1958 0.2384 REMARK 3 13 1.3700 - 1.3300 1.00 2666 140 0.2191 0.2373 REMARK 3 14 1.3300 - 1.3000 1.00 2640 139 0.2356 0.2734 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.410 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 : 0.011 1347 REMARK 3 ANGLE : 1.126 1834 REMARK 3 CHIRALITY : 0.096 217 REMARK 3 PLANARITY : 0.006 235 REMARK 3 DIHEDRAL : 11.573 506 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 8YO0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-MAR-24. REMARK 100 THE DEPOSITION ID IS D_1300046030. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JAN-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 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 : 39490 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 15.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 1.02500 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 (%): 40.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SPG PH 5.0, 27.5% PEG 1500, VAPOR REMARK 280 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 20.39350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.29850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.80300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.29850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.39350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.80300 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 TOTAL BURIED SURFACE AREA: 900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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 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 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 7 CG CD OE1 OE2 REMARK 470 LYS A 36 CG CD CE NZ REMARK 470 TYR A 38 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 39 CD CE NZ REMARK 470 GLU A 69 CD OE1 OE2 REMARK 470 GLU A 70 CG CD OE1 OE2 REMARK 470 LYS A 76 CE NZ REMARK 470 GLU A 95 CD OE1 OE2 REMARK 470 GLU A 110 CG CD OE1 OE2 REMARK 470 GLU A 134 CG CD OE1 OE2 REMARK 470 LYS A 141 CE NZ REMARK 470 LYS A 172 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 ARG A 146 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES 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 GDP A 201 O3B 89.9 REMARK 620 3 HOH A 309 O 176.3 93.3 REMARK 620 4 HOH A 319 O 93.6 88.6 88.5 REMARK 620 5 HOH A 320 O 87.8 89.4 90.2 177.6 REMARK 620 6 HOH A 405 O 88.7 176.7 88.2 88.5 93.5 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8YL3 RELATED DB: PDB REMARK 900 WILDTYPE PROTEIN DBREF 8YO0 A 7 172 UNP Q9ULC3 RAB23_HUMAN 7 172 SEQADV 8YO0 SER A 6 UNP Q9ULC3 EXPRESSION TAG SEQADV 8YO0 A UNP Q9ULC3 TYR 79 DELETION SEQRES 1 A 166 SER GLU VAL ALA ILE LYS MET VAL VAL VAL GLY ASN GLY SEQRES 2 A 166 ALA VAL GLY LYS SER SER MET ILE GLN ARG TYR CYS LYS SEQRES 3 A 166 GLY ILE PHE THR LYS ASP TYR LYS LYS THR ILE GLY VAL SEQRES 4 A 166 ASP PHE LEU GLU ARG GLN ILE GLN VAL ASN ASP GLU ASP SEQRES 5 A 166 VAL ARG LEU MET LEU TRP ASP THR ALA GLY GLN GLU GLU SEQRES 6 A 166 PHE ASP ALA ILE THR LYS ALA TYR ARG GLY ALA GLN ALA SEQRES 7 A 166 CYS VAL LEU VAL PHE SER THR THR ASP ARG GLU SER PHE SEQRES 8 A 166 GLU ALA VAL SER SER TRP ARG GLU LYS VAL VAL ALA GLU SEQRES 9 A 166 VAL GLY ASP ILE PRO THR VAL LEU VAL GLN ASN LYS ILE SEQRES 10 A 166 ASP LEU LEU ASP ASP SER CYS ILE LYS ASN GLU GLU ALA SEQRES 11 A 166 GLU ALA LEU ALA LYS ARG LEU LYS LEU ARG PHE TYR ARG SEQRES 12 A 166 THR SER VAL LYS GLU ASP LEU ASN VAL ASN GLU VAL PHE SEQRES 13 A 166 LYS TYR LEU ALA GLU LYS TYR LEU GLN LYS HET GDP A 201 28 HET MG A 202 1 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 MG MG 2+ FORMUL 4 HOH *172(H2 O) HELIX 1 AA1 GLY A 21 GLY A 32 1 12 HELIX 2 AA2 GLY A 67 PHE A 71 5 5 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 PHE A 46 VAL A 53 0 SHEET 2 AA1 6 GLU A 56 TRP A 63 -1 O LEU A 62 N LEU A 47 SHEET 3 AA1 6 VAL A 8 GLY A 16 1 N MET A 12 O MET A 61 SHEET 4 AA1 6 ALA A 84 SER A 90 1 O VAL A 86 N VAL A 15 SHEET 5 AA1 6 THR A 116 ASN A 121 1 O ASN A 121 N PHE A 89 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 2.08 LINK O3B GDP A 201 MG MG A 202 1555 1555 2.03 LINK MG MG A 202 O HOH A 309 1555 1555 2.07 LINK MG MG A 202 O HOH A 319 1555 1555 2.09 LINK MG MG A 202 O HOH A 320 1555 1555 2.06 LINK MG MG A 202 O HOH A 405 1555 1555 2.08 CRYST1 40.787 51.606 74.597 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 0.024518 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019378 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013405 0.00000