HEADER OXIDOREDUCTASE 12-SEP-21 7VFC TITLE CRYSTAL STRUCTURE OF CPMO2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CPMO2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: COMPOST METAGENOME; SOURCE 3 ORGANISM_TAXID: 702656; SOURCE 4 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 4922 KEYWDS LYTIC POLYSACCHARIDE MONOOXYGENASES, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR D.LIU REVDAT 2 29-NOV-23 7VFC 1 REMARK REVDAT 1 14-SEP-22 7VFC 0 JRNL AUTH D.LIU JRNL TITL CRYSTAL STRUCTURE OF CPMO2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.21 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.420 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 67508 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 3330 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 3.4900 - 2.7700 0.99 2741 131 0.1588 0.1762 REMARK 3 2 2.7700 - 2.4200 0.98 2668 140 0.1660 0.1742 REMARK 3 3 2.4200 - 2.2000 0.99 2681 144 0.1619 0.1876 REMARK 3 4 2.2000 - 2.0400 0.99 2671 160 0.1541 0.1908 REMARK 3 5 2.0400 - 1.9200 0.98 2645 150 0.1512 0.1812 REMARK 3 6 1.9200 - 1.8300 0.99 2685 142 0.1521 0.1875 REMARK 3 7 1.8300 - 1.7500 0.99 2653 140 0.1518 0.1746 REMARK 3 8 1.7500 - 1.6800 0.99 2707 135 0.1542 0.1881 REMARK 3 9 1.6800 - 1.6200 0.99 2669 138 0.1473 0.1673 REMARK 3 10 1.6200 - 1.5700 0.99 2681 112 0.1456 0.1614 REMARK 3 11 1.5700 - 1.5300 0.99 2688 141 0.1380 0.1534 REMARK 3 12 1.5300 - 1.4900 0.99 2669 160 0.1354 0.1885 REMARK 3 13 1.4900 - 1.4500 0.99 2643 153 0.1418 0.1501 REMARK 3 14 1.4500 - 1.4200 0.99 2674 124 0.1370 0.1646 REMARK 3 15 1.4200 - 1.3900 0.99 2702 124 0.1415 0.1691 REMARK 3 16 1.3900 - 1.3600 0.99 2636 133 0.1359 0.1837 REMARK 3 17 1.3600 - 1.3300 0.98 2655 152 0.1510 0.1928 REMARK 3 18 1.3300 - 1.3100 0.99 2668 146 0.1506 0.1861 REMARK 3 19 1.3100 - 1.2900 0.99 2692 137 0.1517 0.2162 REMARK 3 20 1.2900 - 1.2700 0.99 2635 141 0.1543 0.1841 REMARK 3 21 1.2700 - 1.2500 0.99 2690 135 0.1527 0.1836 REMARK 3 22 1.2500 - 1.2300 0.99 2660 122 0.1565 0.1884 REMARK 3 23 1.2300 - 1.2100 0.95 2593 133 0.1640 0.1932 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.283 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.51 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 1761 REMARK 3 ANGLE : 0.809 2424 REMARK 3 CHIRALITY : 0.082 267 REMARK 3 PLANARITY : 0.005 322 REMARK 3 DIHEDRAL : 3.803 913 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 7VFC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1300024441. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUL-21 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 : BL18U1 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 EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 67508 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.210 REMARK 200 RESOLUTION RANGE LOW (A) : 29.820 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.25 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHENIX REMARK 200 STARTING MODEL: 6H1Z REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG3350,0.1 M TRIS-HCL, PH8.5,0.2M REMARK 280 AMMONIUM ACETATE, VAPOR DIFFUSION, TEMPERATURE 291K 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 25.61150 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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: 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 GLU A 21 -49.93 -135.43 REMARK 500 HIS A 57 178.02 85.36 REMARK 500 ASP A 137 55.52 -93.92 REMARK 500 ASP A 214 124.24 -38.57 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 720 DISTANCE = 7.23 ANGSTROMS 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 CU A 302 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 1 NE2 REMARK 620 2 HIS A 86 NE2 90.3 REMARK 620 N 1 DBREF 7VFC A 1 228 PDB 7VFC 7VFC 1 228 SEQRES 1 A 228 HIS GLY PHE VAL SER GLY ILE VAL ALA ASP GLY SER TYR SEQRES 2 A 228 TYR GLY GLY TYR ASN THR ASP GLU TYR PRO TYR MET SER SEQRES 3 A 228 ASN PRO PRO ASN VAL ILE ALA TRP SER THR THR ALA THR SEQRES 4 A 228 ASN CYS GLY PHE THR ASN GLY THR GLY TYR GLN SER PRO SEQRES 5 A 228 ASP ILE ILE CYS HIS SER ASN ALA SER ASN GLY SER ASN SEQRES 6 A 228 THR ALA VAL VAL ALA ALA GLY SER SER ILE GLN PHE GLN SEQRES 7 A 228 TRP THR VAL TRP PRO ALA SER HIS HIS GLY PRO LEU ILE SEQRES 8 A 228 THR TYR LEU ALA PRO CYS GLY GLY ASN CYS ALA THR VAL SEQRES 9 A 228 ASP LYS THR THR LEU ASP PHE THR LYS ILE ALA ALA VAL SEQRES 10 A 228 GLY LEU VAL ASN GLY VAL SER PRO PRO GLY VAL TRP ALA SEQRES 11 A 228 ASP ASP SER MET ILE ALA ASP ASN ASN THR ALA VAL VAL SEQRES 12 A 228 VAL ILE PRO ALA SER TYR ALA PRO GLY ASN TYR VAL LEU SEQRES 13 A 228 ARG HIS GLU ILE ILE ALA LEU HIS VAL ALA GLY ASN ASN SEQRES 14 A 228 ASN GLY ALA GLN ASN TYR PRO GLN CYS PHE ASN ILE GLN SEQRES 15 A 228 ILE THR GLY GLY GLY SER ALA GLN GLY SER GLY VAL ALA SEQRES 16 A 228 GLY THR SER LEU TYR LYS ASN THR ASP PRO GLY ILE LYS SEQRES 17 A 228 PHE ASN ILE TYR SER ASP LEU SER GLY GLY TYR PRO ILE SEQRES 18 A 228 PRO GLY PRO ALA LEU PHE ALA HET PEG A 301 7 HET CU A 302 1 HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM CU COPPER (II) ION FORMUL 2 PEG C4 H10 O3 FORMUL 3 CU CU 2+ FORMUL 4 HOH *320(H2 O) HELIX 1 AA1 GLU A 21 MET A 25 5 5 HELIX 2 AA2 ASN A 45 TYR A 49 5 5 HELIX 3 AA3 PRO A 52 HIS A 57 1 6 HELIX 4 AA4 ASP A 105 THR A 108 5 4 HELIX 5 AA5 ALA A 130 ASP A 137 1 8 HELIX 6 AA6 THR A 197 LEU A 199 5 3 SHEET 1 AA1 4 SER A 12 GLY A 15 0 SHEET 2 AA1 4 VAL A 4 ALA A 9 -1 N ALA A 9 O SER A 12 SHEET 3 AA1 4 SER A 74 TRP A 79 -1 O GLN A 78 N GLY A 6 SHEET 4 AA1 4 THR A 140 VAL A 144 -1 O ALA A 141 N PHE A 77 SHEET 1 AA2 6 ALA A 67 ALA A 70 0 SHEET 2 AA2 6 GLN A 173 THR A 184 1 O GLN A 182 N VAL A 69 SHEET 3 AA2 6 GLY A 152 ALA A 162 -1 N LEU A 156 O PHE A 179 SHEET 4 AA2 6 LEU A 90 PRO A 96 -1 N ILE A 91 O GLU A 159 SHEET 5 AA2 6 ASP A 110 VAL A 117 -1 O ALA A 115 N THR A 92 SHEET 6 AA2 6 VAL A 194 ALA A 195 -1 O VAL A 194 N PHE A 111 SHEET 1 AA3 2 LEU A 119 ASN A 121 0 SHEET 2 AA3 2 VAL A 128 TRP A 129 -1 O VAL A 128 N VAL A 120 SSBOND 1 CYS A 56 CYS A 178 1555 1555 2.04 SSBOND 2 CYS A 97 CYS A 101 1555 1555 2.02 LINK NE2 HIS A 1 CU CU A 302 1555 1555 1.94 LINK NE2 HIS A 86 CU CU A 302 1555 1555 2.21 CISPEP 1 PRO A 125 PRO A 126 0 9.73 CRYST1 39.392 51.223 57.133 90.00 99.34 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 0.025386 0.000000 0.004176 0.00000 SCALE2 0.000000 0.019522 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017738 0.00000