HEADER LYASE 11-SEP-23 8WC1 TITLE A CARBOHYDRATE BINDING DOMAIN OF A PUTATIVE PECTATE LYASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PECTATE LYASE FAMILY 9; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MONOGLOBUS PECTINILYTICUS; SOURCE 3 ORGANISM_TAXID: 1981510; SOURCE 4 GENE: B9O19_00428; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS CARBOHYDRATE BINDING, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR G.C.LIU,Y.G.CHANG REVDAT 1 18-SEP-24 8WC1 0 JRNL AUTH G.C.LIU,Y.G.CHANG JRNL TITL STRUCTURE OF A CARBOHYDRATE BINDING DOMAIN AT 1.30 ANGSTROMS JRNL TITL 2 RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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) : 34.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 37241 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.370 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 34.8200 - 3.1300 1.00 2689 153 0.1533 0.1832 REMARK 3 2 3.1300 - 2.4900 1.00 2559 145 0.1898 0.1781 REMARK 3 3 2.4900 - 2.1700 1.00 2554 145 0.1722 0.1799 REMARK 3 4 2.1700 - 1.9700 1.00 2527 144 0.1615 0.1681 REMARK 3 5 1.9700 - 1.8300 1.00 2515 142 0.1681 0.1655 REMARK 3 6 1.8300 - 1.7200 1.00 2505 142 0.1735 0.2074 REMARK 3 7 1.7200 - 1.6400 1.00 2501 142 0.1678 0.1701 REMARK 3 8 1.6400 - 1.5700 1.00 2499 142 0.1651 0.1726 REMARK 3 9 1.5700 - 1.5100 1.00 2476 140 0.1737 0.2208 REMARK 3 10 1.5100 - 1.4500 1.00 2494 142 0.1774 0.1951 REMARK 3 11 1.4500 - 1.4100 1.00 2474 140 0.1823 0.1896 REMARK 3 12 1.4100 - 1.3700 1.00 2470 140 0.1857 0.1960 REMARK 3 13 1.3700 - 1.3300 1.00 2483 142 0.2022 0.2039 REMARK 3 14 1.3300 - 1.3000 1.00 2495 141 0.2206 0.2617 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 17.790 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 : 0.005 NULL REMARK 3 ANGLE : 0.897 NULL REMARK 3 CHIRALITY : 0.083 184 REMARK 3 PLANARITY : 0.006 200 REMARK 3 DIHEDRAL : 6.390 161 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 8WC1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 14-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1300039254. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUL-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) : 0.979 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 : 37307 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 42.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.1000 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 : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.29700 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 (%): 36.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28% W/V PEG MME 2000, 0.1M BIS-TRIS REMARK 280 PH6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 19.97850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.51150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.09500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.51150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.97850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.09500 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 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 MET A -1 REMARK 465 GLY A 0 REMARK 465 ASP A 152 REMARK 465 PRO A 153 REMARK 465 VAL A 154 REMARK 465 TYR A 155 REMARK 465 ASP A 156 REMARK 465 PHE A 157 REMARK 465 GLU A 158 REMARK 465 ASP A 159 REMARK 465 LEU A 160 REMARK 465 ASN A 161 REMARK 465 GLY A 162 REMARK 465 VAL A 163 REMARK 465 VAL A 164 REMARK 465 LEU A 165 REMARK 465 GLU A 166 REMARK 465 PRO A 167 REMARK 465 MET A 168 REMARK 465 LEU A 169 REMARK 465 GLU A 170 REMARK 465 HIS A 171 REMARK 465 HIS A 172 REMARK 465 HIS A 173 REMARK 465 HIS A 174 REMARK 465 HIS A 175 REMARK 465 HIS A 176 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 O HOH A 311 O HOH A 449 1.85 REMARK 500 O HOH A 391 O HOH A 412 1.94 REMARK 500 O HOH A 383 O HOH A 406 1.98 REMARK 500 O HOH A 385 O HOH A 409 2.02 REMARK 500 O HOH A 386 O HOH A 412 2.05 REMARK 500 O HOH A 306 O HOH A 399 2.08 REMARK 500 O HOH A 418 O HOH A 421 2.09 REMARK 500 O HOH A 276 O HOH A 277 2.12 REMARK 500 O HOH A 202 O HOH A 387 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 246 O HOH A 290 4455 2.09 REMARK 500 O HOH A 324 O HOH A 457 1655 2.10 REMARK 500 O HOH A 377 O HOH A 402 3555 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 ALA A 112 -155.93 -123.58 REMARK 500 SER A 135 -158.22 64.37 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8WC1 A 1 168 UNP A0A2K9P019_9FIRM DBREF2 8WC1 A A0A2K9P019 30 197 SEQADV 8WC1 MET A -1 UNP A0A2K9P01 INITIATING METHIONINE SEQADV 8WC1 GLY A 0 UNP A0A2K9P01 EXPRESSION TAG SEQADV 8WC1 LEU A 169 UNP A0A2K9P01 EXPRESSION TAG SEQADV 8WC1 GLU A 170 UNP A0A2K9P01 EXPRESSION TAG SEQADV 8WC1 HIS A 171 UNP A0A2K9P01 EXPRESSION TAG SEQADV 8WC1 HIS A 172 UNP A0A2K9P01 EXPRESSION TAG SEQADV 8WC1 HIS A 173 UNP A0A2K9P01 EXPRESSION TAG SEQADV 8WC1 HIS A 174 UNP A0A2K9P01 EXPRESSION TAG SEQADV 8WC1 HIS A 175 UNP A0A2K9P01 EXPRESSION TAG SEQADV 8WC1 HIS A 176 UNP A0A2K9P01 EXPRESSION TAG SEQRES 1 A 178 MET GLY LEU PRO PRO ASP SER VAL TYR ASN ILE SER ASP SEQRES 2 A 178 MET SER THR GLY THR ILE SER GLN ASP THR GLN ILE GLY SEQRES 3 A 178 ASP PHE SER ILE ILE ALA ALA THR ASP GLY ASN THR ALA SEQRES 4 A 178 ILE ALA VAL ASP GLY ASN LYS LYS THR SER THR THR THR SEQRES 5 A 178 GLY ILE LYS TYR THR LYS ARG LEU LYS LEU ASN GLY THR SEQRES 6 A 178 GLY ASN GLN THR ASN ARG ALA ILE LYS PHE THR ALA SER SEQRES 7 A 178 GLU PRO ALA THR PHE MET ILE GLU ALA ALA SER ALA ASN SEQRES 8 A 178 SER SER ALA VAL ARG THR GLY VAL LEU VAL ASN SER ALA SEQRES 9 A 178 GLY GLU THR VAL ALA SER GLY GLU PHE ALA SER GLY LEU SEQRES 10 A 178 THR TYR LYS LYS MET THR VAL PRO GLU ALA GLY ASP TYR SEQRES 11 A 178 TRP PHE TYR SER THR ASP SER GLY ILE ASN VAL TYR TYR SEQRES 12 A 178 LEU LYS LEU THR TYR GLU VAL GLN PRO PRO ASP PRO VAL SEQRES 13 A 178 TYR ASP PHE GLU ASP LEU ASN GLY VAL VAL LEU GLU PRO SEQRES 14 A 178 MET LEU GLU HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *271(H2 O) HELIX 1 AA1 SER A 10 MET A 12 5 3 SHEET 1 AA1 5 SER A 5 ASN A 8 0 SHEET 2 AA1 5 ILE A 137 THR A 145 -1 O LEU A 144 N SER A 5 SHEET 3 AA1 5 LYS A 53 LYS A 59 -1 N LEU A 58 O VAL A 139 SHEET 4 AA1 5 ILE A 38 THR A 46 -1 N ALA A 39 O LYS A 59 SHEET 5 AA1 5 GLY A 15 ILE A 17 -1 N ILE A 17 O ILE A 38 SHEET 1 AA2 4 SER A 5 ASN A 8 0 SHEET 2 AA2 4 ILE A 137 THR A 145 -1 O LEU A 144 N SER A 5 SHEET 3 AA2 4 ALA A 79 SER A 87 -1 N MET A 82 O LYS A 143 SHEET 4 AA2 4 THR A 116 VAL A 122 -1 O MET A 120 N PHE A 81 SHEET 1 AA3 6 THR A 21 ILE A 23 0 SHEET 2 AA3 6 PHE A 26 ILE A 29 -1 O ILE A 28 N THR A 21 SHEET 3 AA3 6 ALA A 70 ALA A 75 -1 O ALA A 70 N ILE A 29 SHEET 4 AA3 6 GLY A 126 SER A 132 -1 O PHE A 130 N ILE A 71 SHEET 5 AA3 6 ARG A 94 VAL A 99 -1 N VAL A 99 O TRP A 129 SHEET 6 AA3 6 THR A 105 PHE A 111 -1 O VAL A 106 N LEU A 98 CRYST1 39.957 52.190 71.023 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 0.025027 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019161 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014080 0.00000 MASTER 292 0 0 1 15 0 0 6 1398 1 0 14 END