HEADER TRANSFERASE 24-AUG-24 9JAC TITLE GMPK IN COMPLEX WITH GMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: GUANYLATE KINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GMP KINASE,GUANYLATE KINASE 1; COMPND 5 EC: 2.7.4.8; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: GUK1, GMK, GMPK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GUANYLATE KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR L.WANG,K.RUAN REVDAT 2 10-SEP-25 9JAC 1 JRNL REVDAT 1 03-SEP-25 9JAC 0 JRNL AUTH L.WANG,Z.LI,Y.XUAN,J.QIN,S.LI,F.ZHONG,Y.SONG,K.YANG,M.LV, JRNL AUTH 2 F.LI,Z.JIAHAI,Y.PAN,S.GUANG,Y.ZHAO,Y.SHI,X.LIU,Y.DU,J.GAO, JRNL AUTH 3 K.RUAN JRNL TITL COMPREHENSIVE PROFILING OF THE CATALYTIC CONFORMATIONS OF JRNL TITL 2 HUMAN GUANYLATE KINASE. JRNL REF NAT COMMUN V. 16 6859 2025 JRNL REFN ESSN 2041-1723 JRNL PMID 40715061 JRNL DOI 10.1038/S41467-025-61732-Y REMARK 2 REMARK 2 RESOLUTION. 1.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.19_4092: ???) 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) : 1.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 40314 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 2049 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 30.7700 - 3.6300 0.99 2659 154 0.1499 0.1537 REMARK 3 2 3.6200 - 2.8800 0.98 2575 140 0.1592 0.2223 REMARK 3 3 2.8800 - 2.5100 0.99 2594 161 0.1719 0.1936 REMARK 3 4 2.5100 - 2.2800 0.99 2574 160 0.1652 0.2050 REMARK 3 5 2.2800 - 2.1200 0.98 2597 115 0.1475 0.2027 REMARK 3 6 2.1200 - 2.0000 0.98 2564 127 0.1738 0.2085 REMARK 3 7 2.0000 - 1.9000 0.97 2534 114 0.1676 0.2254 REMARK 3 8 1.9000 - 1.8100 0.98 2548 141 0.1492 0.2092 REMARK 3 9 1.8100 - 1.7400 0.99 2555 143 0.1520 0.1963 REMARK 3 10 1.7400 - 1.6800 0.98 2540 147 0.1609 0.2102 REMARK 3 11 1.6800 - 1.6300 0.98 2560 130 0.1635 0.2489 REMARK 3 12 1.6300 - 1.5800 0.97 2529 117 0.1491 0.1821 REMARK 3 13 1.5800 - 1.5400 0.98 2533 138 0.1597 0.2006 REMARK 3 14 1.5400 - 1.5000 0.92 2374 124 0.3178 0.3400 REMARK 3 15 1.5000 - 1.4700 0.97 2529 138 0.2921 0.3652 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.260 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 : 0.007 1553 REMARK 3 ANGLE : 0.929 2112 REMARK 3 CHIRALITY : 0.077 243 REMARK 3 PLANARITY : 0.007 275 REMARK 3 DIHEDRAL : 14.204 584 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 9JAC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 26-AUG-24. REMARK 100 THE DEPOSITION ID IS D_1300050595. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAY-23 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 : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97853 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40564 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.470 REMARK 200 RESOLUTION RANGE LOW (A) : 48.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 9.200 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.50300 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: MOLREP REMARK 200 STARTING MODEL: 1LVG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35% PEG4000, 0.1 M AMMONIUM ACETATE, REMARK 280 0.1 M TRISODIUM CITRATE, PH 6.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 30.37733 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 15.18867 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 22.78300 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 7.59433 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 37.97167 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 ARG A 194 REMARK 465 THR A 195 REMARK 465 GLY A 196 REMARK 465 ALA A 197 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 MET A 1 CG SD CE REMARK 470 ASP A 114 CG OD1 OD2 REMARK 470 ARG A 116 CD NE CZ NH1 NH2 REMARK 470 GLN A 132 CD OE1 NE2 REMARK 470 GLN A 153 CD OE1 NE2 REMARK 470 LYS A 160 CG CD CE NZ REMARK 470 LYS A 190 CG CD CE NZ REMARK 470 LYS A 191 CG CD CE NZ 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 51 -61.07 -122.78 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 583 DISTANCE = 6.19 ANGSTROMS DBREF 9JAC A 1 197 UNP Q16774 KGUA_HUMAN 1 197 SEQADV 9JAC HIS A 0 UNP Q16774 EXPRESSION TAG SEQRES 1 A 198 HIS MET SER GLY PRO ARG PRO VAL VAL LEU SER GLY PRO SEQRES 2 A 198 SER GLY ALA GLY LYS SER THR LEU LEU LYS ARG LEU LEU SEQRES 3 A 198 GLN GLU HIS SER GLY ILE PHE GLY PHE SER VAL SER HIS SEQRES 4 A 198 THR THR ARG ASN PRO ARG PRO GLY GLU GLU ASN GLY LYS SEQRES 5 A 198 ASP TYR TYR PHE VAL THR ARG GLU VAL MET GLN ARG ASP SEQRES 6 A 198 ILE ALA ALA GLY ASP PHE ILE GLU HIS ALA GLU PHE SER SEQRES 7 A 198 GLY ASN LEU TYR GLY THR SER LYS VAL ALA VAL GLN ALA SEQRES 8 A 198 VAL GLN ALA MET ASN ARG ILE CYS VAL LEU ASP VAL ASP SEQRES 9 A 198 LEU GLN GLY VAL ARG ASN ILE LYS ALA THR ASP LEU ARG SEQRES 10 A 198 PRO ILE TYR ILE SER VAL GLN PRO PRO SER LEU HIS VAL SEQRES 11 A 198 LEU GLU GLN ARG LEU ARG GLN ARG ASN THR GLU THR GLU SEQRES 12 A 198 GLU SER LEU VAL LYS ARG LEU ALA ALA ALA GLN ALA ASP SEQRES 13 A 198 MET GLU SER SER LYS GLU PRO GLY LEU PHE ASP VAL VAL SEQRES 14 A 198 ILE ILE ASN ASP SER LEU ASP GLN ALA TYR ALA GLU LEU SEQRES 15 A 198 LYS GLU ALA LEU SER GLU GLU ILE LYS LYS ALA GLN ARG SEQRES 16 A 198 THR GLY ALA HET 5GP A 201 24 HET GOL A 202 6 HETNAM 5GP GUANOSINE-5'-MONOPHOSPHATE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 5GP C10 H14 N5 O8 P FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *283(H2 O) HELIX 1 AA1 GLY A 16 HIS A 28 1 13 HELIX 2 AA2 THR A 57 ALA A 67 1 11 HELIX 3 AA3 LYS A 85 MET A 94 1 10 HELIX 4 AA4 ASP A 103 ALA A 112 1 10 HELIX 5 AA5 SER A 126 ASN A 138 1 13 HELIX 6 AA6 THR A 141 SER A 159 1 19 HELIX 7 AA7 SER A 173 LEU A 185 1 13 HELIX 8 AA8 LEU A 185 GLN A 193 1 9 SHEET 1 AA1 5 PHE A 32 PHE A 34 0 SHEET 2 AA1 5 ILE A 97 ASP A 101 1 O VAL A 99 N GLY A 33 SHEET 3 AA1 5 VAL A 7 SER A 10 1 N LEU A 9 O LEU A 100 SHEET 4 AA1 5 ILE A 118 GLN A 123 1 O ILE A 118 N VAL A 8 SHEET 5 AA1 5 VAL A 167 ILE A 170 1 O ILE A 169 N SER A 121 SHEET 1 AA2 4 TYR A 54 PHE A 55 0 SHEET 2 AA2 4 HIS A 38 THR A 39 1 N THR A 39 O TYR A 54 SHEET 3 AA2 4 ASN A 79 SER A 84 -1 O GLY A 82 N HIS A 38 SHEET 4 AA2 4 PHE A 70 PHE A 76 -1 N PHE A 76 O ASN A 79 CRYST1 96.362 96.362 45.566 90.00 90.00 120.00 P 65 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 0.010378 0.005991 0.000000 0.00000 SCALE2 0.000000 0.011983 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021946 0.00000 CONECT 1497 1498 1499 1500 1501 CONECT 1498 1497 CONECT 1499 1497 CONECT 1500 1497 CONECT 1501 1497 1502 CONECT 1502 1501 1503 CONECT 1503 1502 1504 1505 CONECT 1504 1503 1509 CONECT 1505 1503 1506 1507 CONECT 1506 1505 CONECT 1507 1505 1508 1509 CONECT 1508 1507 CONECT 1509 1504 1507 1510 CONECT 1510 1509 1511 1520 CONECT 1511 1510 1512 CONECT 1512 1511 1513 CONECT 1513 1512 1514 1520 CONECT 1514 1513 1515 1516 CONECT 1515 1514 CONECT 1516 1514 1517 CONECT 1517 1516 1518 1519 CONECT 1518 1517 CONECT 1519 1517 1520 CONECT 1520 1510 1513 1519 CONECT 1521 1522 1523 CONECT 1522 1521 CONECT 1523 1521 1524 1525 CONECT 1524 1523 CONECT 1525 1523 1526 CONECT 1526 1525 MASTER 266 0 2 8 9 0 0 6 1793 1 30 16 END