HEADER TRANSFERASE 24-AUG-24 9JAD TITLE GMPK IN COMPLEX WITH GMP AND K+ 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 9JAD 1 JRNL REVDAT 1 03-SEP-25 9JAD 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. 1.55 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 34157 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.580 REMARK 3 FREE R VALUE TEST SET COUNT : 1565 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 31.5100 - 3.4500 1.00 3137 139 0.1555 0.1790 REMARK 3 2 3.4400 - 2.7400 1.00 3060 143 0.1721 0.1938 REMARK 3 3 2.7400 - 2.3900 1.00 3061 135 0.1748 0.2357 REMARK 3 4 2.3900 - 2.1700 1.00 3020 143 0.1637 0.2034 REMARK 3 5 2.1700 - 2.0200 1.00 3005 159 0.1507 0.2020 REMARK 3 6 2.0200 - 1.9000 0.99 3001 130 0.1522 0.1999 REMARK 3 7 1.9000 - 1.8000 0.98 2941 164 0.1625 0.2229 REMARK 3 8 1.8000 - 1.7200 0.97 2919 154 0.1818 0.2481 REMARK 3 9 1.7200 - 1.6600 0.96 2900 120 0.1869 0.2274 REMARK 3 10 1.6600 - 1.6000 0.93 2837 130 0.1933 0.2291 REMARK 3 11 1.6000 - 1.5500 0.91 2711 148 0.2191 0.3106 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.680 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 : 0.008 1538 REMARK 3 ANGLE : 1.004 2089 REMARK 3 CHIRALITY : 0.059 239 REMARK 3 PLANARITY : 0.008 274 REMARK 3 DIHEDRAL : 7.800 223 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 9JAD 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_1300050593. 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 : 35047 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 48.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.500 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.39500 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 (%): 55.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.77 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 30.28467 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 15.14233 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 22.71350 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 7.57117 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 37.85583 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 HIS A 0 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 GLN A 26 CD OE1 NE2 REMARK 470 GLU A 59 CD OE1 OE2 REMARK 470 ARG A 116 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 132 CD OE1 NE2 REMARK 470 GLU A 157 CD OE1 OE2 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 -60.73 -122.07 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 K A 201 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 37 OG REMARK 620 2 ASP A 101 O 107.7 REMARK 620 3 ASP A 101 OD1 150.8 68.5 REMARK 620 4 HOH A 392 O 77.1 159.6 97.3 REMARK 620 5 HOH A 406 O 138.7 99.6 68.5 87.9 REMARK 620 6 HOH A 411 O 76.5 79.4 74.3 82.7 140.0 REMARK 620 N 1 2 3 4 5 DBREF 9JAD A 1 197 UNP Q16774 KGUA_HUMAN 1 197 SEQADV 9JAD 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 K A 201 1 HET 5GP A 202 24 HET ACT A 203 4 HETNAM K POTASSIUM ION HETNAM 5GP GUANOSINE-5'-MONOPHOSPHATE HETNAM ACT ACETATE ION FORMUL 2 K K 1+ FORMUL 3 5GP C10 H14 N5 O8 P FORMUL 4 ACT C2 H3 O2 1- FORMUL 5 HOH *230(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 LINK OG SER A 37 K K A 201 1555 1555 2.90 LINK O ASP A 101 K K A 201 1555 1555 2.64 LINK OD1 ASP A 101 K K A 201 1555 1555 2.75 LINK K K A 201 O HOH A 392 1555 1555 2.87 LINK K K A 201 O HOH A 406 1555 1555 2.76 LINK K K A 201 O HOH A 411 1555 1555 2.86 CRYST1 96.252 96.252 45.427 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 0.010389 0.005998 0.000000 0.00000 SCALE2 0.000000 0.011997 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022013 0.00000 CONECT 271 1486 CONECT 777 1486 CONECT 780 1486 CONECT 1486 271 777 780 1606 CONECT 1486 1620 1625 CONECT 1487 1488 1489 1490 1491 CONECT 1488 1487 CONECT 1489 1487 CONECT 1490 1487 CONECT 1491 1487 1492 CONECT 1492 1491 1493 CONECT 1493 1492 1494 1495 CONECT 1494 1493 1499 CONECT 1495 1493 1496 1497 CONECT 1496 1495 CONECT 1497 1495 1498 1499 CONECT 1498 1497 CONECT 1499 1494 1497 1500 CONECT 1500 1499 1501 1510 CONECT 1501 1500 1502 CONECT 1502 1501 1503 CONECT 1503 1502 1504 1510 CONECT 1504 1503 1505 1506 CONECT 1505 1504 CONECT 1506 1504 1507 CONECT 1507 1506 1508 1509 CONECT 1508 1507 CONECT 1509 1507 1510 CONECT 1510 1500 1503 1509 CONECT 1511 1512 1513 1514 CONECT 1512 1511 CONECT 1513 1511 CONECT 1514 1511 CONECT 1606 1486 CONECT 1620 1486 CONECT 1625 1486 MASTER 265 0 3 8 9 0 0 6 1728 1 36 16 END