HEADER CYTOSOLIC PROTEIN 16-JUL-19 6KHU TITLE THE CRYSTAL STRUCTURE OF A DGC PROTEIN FROM THERMOTOGA MARITIMA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIGUANYLATE CYCLASE/PHOSPHODIESTERASE-DOMAIN CONTAINING COMPND 3 PROTEIN; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA MSB8; SOURCE 3 ORGANISM_TAXID: 243274; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_VARIANT: STAR; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PHIS2 KEYWDS PUTATIVE DIGUANYLATE CYCLASE, CYTOSOLIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.W.BEEN,H.J.YOON,H.H.LEE REVDAT 1 22-JUL-20 6KHU 0 JRNL AUTH K.W.BEEN,H.J.YOON,H.H.LEE JRNL TITL CRYSTAL STRUCTURE OF A DGC PROTEIN FROM THERMOTOGA MARITIMA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 21394 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.060 REMARK 3 FREE R VALUE TEST SET COUNT : 2152 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 29.5444 - 5.1652 0.98 1275 144 0.2062 0.2173 REMARK 3 2 5.1652 - 4.1033 1.00 1298 146 0.1577 0.2018 REMARK 3 3 4.1033 - 3.5856 0.99 1266 148 0.1755 0.2086 REMARK 3 4 3.5856 - 3.2582 0.98 1274 142 0.2016 0.2520 REMARK 3 5 3.2582 - 3.0249 1.00 1298 150 0.1973 0.2450 REMARK 3 6 3.0249 - 2.8467 1.00 1295 145 0.2043 0.2559 REMARK 3 7 2.8467 - 2.7043 1.00 1282 144 0.1995 0.2438 REMARK 3 8 2.7043 - 2.5866 1.00 1299 140 0.1897 0.2291 REMARK 3 9 2.5866 - 2.4871 1.00 1297 148 0.1989 0.2137 REMARK 3 10 2.4871 - 2.4013 1.00 1279 145 0.1919 0.2457 REMARK 3 11 2.4013 - 2.3263 0.99 1287 139 0.2118 0.2892 REMARK 3 12 2.3263 - 2.2598 0.97 1254 139 0.2074 0.2500 REMARK 3 13 2.2598 - 2.2003 1.00 1289 145 0.2418 0.3097 REMARK 3 14 2.2003 - 2.1467 0.96 1234 135 0.2137 0.2883 REMARK 3 15 2.1467 - 2.0980 1.00 1315 142 0.2018 0.2363 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.410 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.35 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.48 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 1086 REMARK 3 ANGLE : 0.847 1462 REMARK 3 CHIRALITY : 0.056 162 REMARK 3 PLANARITY : 0.005 186 REMARK 3 DIHEDRAL : 7.532 665 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: THE STRUCTURE FACTOR FILE CONTAINS REMARK 3 FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS REMARK 4 REMARK 4 6KHU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1300013014. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9789 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER SMART 6500 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21596 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.098 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 14.50 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 14.70 REMARK 200 R MERGE FOR SHELL (I) : 0.45400 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: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3000, TRISODIUM CITRATE, ZINC REMARK 280 ACETATE, PH 5.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.57150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.65150 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.65150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 75.85725 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.65150 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.65150 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.28575 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.65150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.65150 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 75.85725 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.65150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.65150 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 25.28575 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 50.57150 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: 70 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 SG CYS A 117 O HOH A 375 2.13 REMARK 500 NH1 ARG A 119 O HOH A 301 2.17 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 ZN A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 116 OE1 REMARK 620 2 HIS A 155 NE2 108.1 REMARK 620 3 GLU A 84 OE1 19.8 89.1 REMARK 620 4 HOH A 354 O 100.7 104.3 100.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 177 OD2 REMARK 620 2 HOH A 371 O 106.0 REMARK 620 3 HIS A 70 ND1 95.0 99.5 REMARK 620 4 HOH A 361 O 104.6 133.6 43.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 202 DBREF 6KHU A 60 190 UNP R4NMR2 R4NMR2_THEMA 60 190 SEQRES 1 A 131 ASP PRO LEU THR ARG VAL TYR ALA LYS ASP HIS PHE LEU SEQRES 2 A 131 ARG LEU LEU SER TYR GLN HIS GLN ARG ALA PHE GLU GLU SEQRES 3 A 131 ASN THR PRO TYR THR ILE PHE PHE VAL LYS THR LYS VAL SEQRES 4 A 131 SER LYS ASN GLU ARG GLU LYS ALA LEU MSE LYS ILE GLY SEQRES 5 A 131 LYS ILE LEU LYS GLU CYS VAL ARG VAL PRO LEU ASP SER SEQRES 6 A 131 VAL GLY ARG TYR SER ASP ASP THR PHE ALA LEU PHE VAL SEQRES 7 A 131 ILE GLY VAL GLY LYS GLU THR ALA PRO ASN ILE GLU GLU SEQRES 8 A 131 ARG ILE LYS ASN HIS ILE GLU SER ILE GLY GLY ILE GLU SEQRES 9 A 131 TYR SER ILE ALA TYR LYS SER TYR PRO GLU ASP PHE MSE SEQRES 10 A 131 ASP LEU GLU LYS ALA ILE LEU ASP LEU GLU LYS ALA VAL SEQRES 11 A 131 ALA MODRES 6KHU MSE A 108 MET MODIFIED RESIDUE MODRES 6KHU MSE A 176 MET MODIFIED RESIDUE HET MSE A 108 8 HET MSE A 176 8 HET ZN A 201 1 HET ZN A 202 1 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 2 ZN 2(ZN 2+) FORMUL 4 HOH *88(H2 O) HELIX 1 AA1 ASP A 60 ARG A 64 5 5 HELIX 2 AA2 LYS A 68 ASN A 86 1 19 HELIX 3 AA3 SER A 99 CYS A 117 1 19 HELIX 4 AA4 THR A 144 GLY A 160 1 17 HELIX 5 AA5 ASP A 177 ALA A 190 1 14 SHEET 1 AA1 5 TYR A 66 ALA A 67 0 SHEET 2 AA1 5 SER A 124 ARG A 127 1 O ARG A 127 N TYR A 66 SHEET 3 AA1 5 THR A 132 ILE A 138 -1 O ALA A 134 N GLY A 126 SHEET 4 AA1 5 TYR A 89 THR A 96 -1 N PHE A 92 O LEU A 135 SHEET 5 AA1 5 TYR A 164 TYR A 171 -1 O TYR A 171 N TYR A 89 LINK C LEU A 107 N MSE A 108 1555 1555 1.33 LINK C MSE A 108 N LYS A 109 1555 1555 1.34 LINK OE1 GLU A 116 ZN ZN A 202 1555 1555 2.02 LINK NE2 HIS A 155 ZN ZN A 202 1555 1555 2.03 LINK C PHE A 175 N MSE A 176 1555 1555 1.33 LINK C MSE A 176 N ASP A 177 1555 1555 1.33 LINK OD2 ASP A 177 ZN ZN A 201 1555 1555 1.95 LINK ZN ZN A 201 O HOH A 371 1555 1555 2.27 LINK ND1 HIS A 70 ZN ZN A 201 1555 4545 2.14 LINK OE1 GLU A 84 ZN ZN A 202 1555 6445 1.99 LINK ZN ZN A 201 O HOH A 361 1555 3444 2.14 LINK ZN ZN A 202 O HOH A 354 1555 6545 2.13 CISPEP 1 TYR A 171 PRO A 172 0 2.12 SITE 1 AC1 4 HIS A 70 ASP A 177 HOH A 361 HOH A 371 SITE 1 AC2 4 GLU A 84 GLU A 116 HIS A 155 HOH A 354 CRYST1 61.303 61.303 101.143 90.00 90.00 90.00 P 43 21 2 8 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 0.016312 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016312 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009887 0.00000