HEADER TRANSFERASE 14-SEP-20 7D18 TITLE CRYSTAL STRUCTURE OF ACIDOBACTERIALES BACTERIUM GLUTAMINYL CYCLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDASE M28; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACIDOBACTERIALES BACTERIUM 59-55; SOURCE 3 ORGANISM_TAXID: 1895690; SOURCE 4 GENE: BGO25_06485; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GLUTAMINYL CYCLASE, METAL BINDING PROTEIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR K.-F.HUANG,J.-S.HUANG,M.-L.WU,W.-L.HSIEH,A.H.-J.WANG REVDAT 3 27-MAR-24 7D18 1 REMARK REVDAT 2 05-MAY-21 7D18 1 JRNL REVDAT 1 14-APR-21 7D18 0 JRNL AUTH K.F.HUANG,J.S.HUANG,M.L.WU,W.L.HSIEH,K.C.HSU,H.L.HSU,T.P.KO, JRNL AUTH 2 A.H.WANG JRNL TITL A UNIQUE CARBOXYLIC-ACID HYDROGEN-BOND NETWORK (CAHBN) JRNL TITL 2 CONFERS GLUTAMINYL CYCLASE ACTIVITY ON M28 FAMILY ENZYMES. JRNL REF J.MOL.BIOL. V. 433 66960 2021 JRNL REFN ESSN 1089-8638 JRNL PMID 33774034 JRNL DOI 10.1016/J.JMB.2021.166960 REMARK 2 REMARK 2 RESOLUTION. 1.33 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 1.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 53489 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.115 REMARK 3 R VALUE (WORKING SET) : 0.114 REMARK 3 FREE R VALUE : 0.140 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.740 REMARK 3 FREE R VALUE TEST SET COUNT : 2003 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 25.9090 - 3.2091 1.00 3803 147 0.1248 0.1248 REMARK 3 2 3.2091 - 2.5479 1.00 3765 150 0.1290 0.1618 REMARK 3 3 2.5479 - 2.2260 1.00 3762 140 0.1183 0.1558 REMARK 3 4 2.2260 - 2.0226 1.00 3749 141 0.1011 0.1283 REMARK 3 5 2.0226 - 1.8777 1.00 3712 152 0.0932 0.1252 REMARK 3 6 1.8777 - 1.7670 0.99 3705 142 0.0945 0.1554 REMARK 3 7 1.7670 - 1.6785 0.99 3745 140 0.0898 0.1241 REMARK 3 8 1.6785 - 1.6054 0.99 3669 148 0.0822 0.1097 REMARK 3 9 1.6054 - 1.5436 0.99 3696 151 0.0826 0.1390 REMARK 3 10 1.5436 - 1.4904 0.98 3696 133 0.0878 0.1272 REMARK 3 11 1.4904 - 1.4438 0.98 3681 144 0.0990 0.1517 REMARK 3 12 1.4438 - 1.4025 0.98 3653 140 0.1168 0.1710 REMARK 3 13 1.4025 - 1.3656 0.98 3637 151 0.1250 0.1922 REMARK 3 14 1.3656 - 1.3323 0.86 3213 124 0.1305 0.1802 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 11.860 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.73 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.52 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7D18 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1300018575. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL15A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53659 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.330 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 (%) : 98.5 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : 0.10700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.77500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.900 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 (%): 31.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M (NH4)2SO4, 0.1 M SODIUM REMARK 280 CACODYLATE, PH 6.5, 30% (W/V) PEG 8000, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 39.16500 REMARK 290 SMTRY3 2 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 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: 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 ASP A 170 75.59 -114.06 REMARK 500 SER A 171 158.88 176.72 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 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 127 OD2 REMARK 620 2 GLU A 161 OE2 107.9 REMARK 620 3 HIS A 276 NE2 99.7 117.7 REMARK 620 4 HOH A 533 O 103.8 122.5 102.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 202 OD2 REMARK 620 2 ASP A 204 O 83.8 REMARK 620 3 ASP A 260 OD1 97.2 134.0 REMARK 620 4 ASP A 260 OD2 85.7 82.8 51.6 REMARK 620 5 ASP A 262 O 84.4 148.1 76.9 125.6 REMARK 620 6 HOH A 597 O 98.1 80.8 143.3 162.7 71.7 REMARK 620 7 HOH A 754 O 177.8 94.1 83.8 93.3 97.8 82.2 REMARK 620 N 1 2 3 4 5 6 DBREF1 7D18 A 16 308 UNP A0A1Q3QTC5_9BACT DBREF2 7D18 A A0A1Q3QTC5 16 308 SEQRES 1 A 293 ALA GLN LYS ALA PRO ALA GLN ASN SER PRO ALA ARG PHE SEQRES 2 A 293 ASN GLY GLN ALA ALA TYR ASN LEU THR ARG GLN TYR ILE SEQRES 3 A 293 ALA ALA ALA PRO LYS ARG TRP VAL GLY SER PRO GLY HIS SEQRES 4 A 293 ALA LYS ALA GLU ALA PHE ILE LYS ASP HIS PHE LYS PRO SEQRES 5 A 293 GLU ILE ALA GLN GLY ARG PHE GLU THR ASP ARG PHE THR SEQRES 6 A 293 ALA GLY THR PRO ALA GLY LEU LEU GLU MET ARG ASN TYR SEQRES 7 A 293 ILE VAL ARG TYR PRO GLY LYS LYS ASP GLY VAL ILE VAL SEQRES 8 A 293 LEU ALA THR HIS TYR GLU THR ASN TYR PRO LEU ARG ASP SEQRES 9 A 293 ILE ASN PHE VAL GLY ALA ASN ASP GLY GLY SER THR THR SEQRES 10 A 293 ALA LEU LEU ILE GLU MET GLY ASN TYR LEU ARG ALA HIS SEQRES 11 A 293 PRO PRO GLN GLY TYR SER ILE TRP LEU VAL PHE ASP ASP SEQRES 12 A 293 GLY GLU GLU ALA ILE GLN SER TRP SER ALA THR ASP SER SEQRES 13 A 293 LEU TYR GLY THR ARG HIS LEU ALA ALA LYS TRP SER GLN SEQRES 14 A 293 ASP GLY THR LEU LYS LYS ILE LYS ALA PHE LEU LEU ALA SEQRES 15 A 293 ASP MET ILE GLY ASP LYS ASP LEU ASN ILE ASP ARG ASP SEQRES 16 A 293 ALA ASN SER THR PRO TRP LEU LEU ASP MET LEU LYS GLN SEQRES 17 A 293 ALA ALA LYS ASN THR GLY HIS SER ALA TYR VAL PHE LYS SEQRES 18 A 293 ASN SER THR ALA VAL GLU ASP ASP HIS LEU PRO PHE ALA SEQRES 19 A 293 LYS ARG GLY VAL PRO VAL LEU ASP ILE ILE ASP ILE ASP SEQRES 20 A 293 TYR GLY PRO ARG THR PHE SER MET PRO ASP GLY TYR HIS SEQRES 21 A 293 HIS THR ALA GLU ASP THR LEU ASP LYS ILE SER ALA HIS SEQRES 22 A 293 SER LEU GLN ILE ALA GLY ASP LEU PHE LEU GLU MET ILE SEQRES 23 A 293 ARG LEU ILE ASN GLN ARG GLY HET ZN A 401 1 HET NA A 402 1 HET SO4 A 403 5 HET SO4 A 404 5 HET SO4 A 405 10 HET SO4 A 406 5 HET SO4 A 407 5 HET SO4 A 408 5 HET SO4 A 409 5 HET GOL A 410 6 HET GOL A 411 6 HET GOL A 412 6 HET GOL A 413 6 HET GOL A 414 6 HET TRS A 415 8 HETNAM ZN ZINC ION HETNAM NA SODIUM ION HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN TRS TRIS BUFFER FORMUL 2 ZN ZN 2+ FORMUL 3 NA NA 1+ FORMUL 4 SO4 7(O4 S 2-) FORMUL 11 GOL 5(C3 H8 O3) FORMUL 16 TRS C4 H12 N O3 1+ FORMUL 17 HOH *331(H2 O) HELIX 1 AA1 ASN A 29 ALA A 44 1 16 HELIX 2 AA2 SER A 51 HIS A 64 1 14 HELIX 3 AA3 PHE A 65 GLY A 72 1 8 HELIX 4 AA4 ASN A 114 ARG A 118 5 5 HELIX 5 AA5 GLY A 128 HIS A 145 1 18 HELIX 6 AA6 LEU A 172 ASP A 185 1 14 HELIX 7 AA7 GLY A 186 LYS A 189 5 4 HELIX 8 AA8 THR A 214 GLY A 229 1 16 HELIX 9 AA9 HIS A 230 ALA A 232 5 3 HELIX 10 AB1 HIS A 245 LYS A 250 1 6 HELIX 11 AB2 THR A 281 ILE A 285 5 5 HELIX 12 AB3 SER A 286 GLY A 308 1 23 SHEET 1 AA1 6 PHE A 74 THR A 83 0 SHEET 2 AA1 6 GLY A 86 TYR A 97 -1 O ASN A 92 N ASP A 77 SHEET 3 AA1 6 TYR A 150 ASP A 157 -1 O PHE A 156 N TYR A 93 SHEET 4 AA1 6 LYS A 101 HIS A 110 1 N THR A 109 O ASP A 157 SHEET 5 AA1 6 ILE A 191 ASP A 198 1 O LEU A 195 N VAL A 106 SHEET 6 AA1 6 VAL A 255 ILE A 259 1 O ILE A 258 N LEU A 196 SHEET 1 AA2 2 ILE A 207 ASP A 210 0 SHEET 2 AA2 2 VAL A 234 THR A 239 1 O PHE A 235 N ILE A 207 LINK OD2 ASP A 127 ZN ZN A 401 1555 1555 1.97 LINK OE2 GLU A 161 ZN ZN A 401 1555 1555 1.90 LINK OD2 ASP A 202 NA NA A 402 1555 1555 2.42 LINK O ASP A 204 NA NA A 402 1555 1555 2.44 LINK OD1 ASP A 260 NA NA A 402 1555 1555 2.63 LINK OD2 ASP A 260 NA NA A 402 1555 1555 2.35 LINK O ASP A 262 NA NA A 402 1555 1555 2.44 LINK NE2 HIS A 276 ZN ZN A 401 1555 1555 2.05 LINK ZN ZN A 401 O HOH A 533 1555 1555 1.94 LINK NA NA A 402 O HOH A 597 1555 1555 2.44 LINK NA NA A 402 O HOH A 754 1555 1555 2.33 CRYST1 37.044 78.330 44.892 90.00 111.15 90.00 P 1 21 1 2 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 0.026995 0.000000 0.010442 0.00000 SCALE2 0.000000 0.012767 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023884 0.00000