HEADER BIOSYNTHETIC PROTEIN 21-JUN-18 6A4X TITLE OXIDASE CHAP-H2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BLEOMYCIN RESISTANCE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DIOXYGENASE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES CURACOI; SOURCE 3 ORGANISM_TAXID: 146536; SOURCE 4 GENE: AQI70_17615; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS VOC FAMILY, DIOXYGENASE, DIMER, CHARTREUSIN, OXIDATIVE REARRANGEMENT, KEYWDS 2 BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.ZHANG,Y.S.WANG,H.M.GE REVDAT 3 22-NOV-23 6A4X 1 LINK REVDAT 2 19-SEP-18 6A4X 1 JRNL REVDAT 1 29-AUG-18 6A4X 0 JRNL AUTH Y.S.WANG,B.ZHANG,J.ZHU,C.L.YANG,Y.GUO,C.L.LIU,F.LIU,H.HUANG, JRNL AUTH 2 S.ZHAO,Y.LIANG,R.H.JIAO,R.X.TAN,H.M.GE JRNL TITL MOLECULAR BASIS FOR THE FINAL OXIDATIVE REARRANGEMENT STEPS JRNL TITL 2 IN CHARTREUSIN BIOSYNTHESIS. JRNL REF J. AM. CHEM. SOC. V. 140 10909 2018 JRNL REFN ESSN 1520-5126 JRNL PMID 30067334 JRNL DOI 10.1021/JACS.8B06623 REMARK 2 REMARK 2 RESOLUTION. 1.63 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.63 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 17434 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 892 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 40.2163 - 2.9618 1.00 3027 158 0.1761 0.2001 REMARK 3 2 2.9618 - 2.3510 0.98 2868 149 0.1944 0.2038 REMARK 3 3 2.3510 - 2.0538 0.98 2775 142 0.1759 0.2050 REMARK 3 4 2.0538 - 1.8660 0.97 2743 164 0.1827 0.2474 REMARK 3 5 1.8660 - 1.7323 0.92 2585 137 0.2165 0.2488 REMARK 3 6 1.7323 - 1.6301 0.91 2544 142 0.2379 0.2594 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.230 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.21 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.97 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 : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 5.1579 17.6335 5.4247 REMARK 3 T TENSOR REMARK 3 T11: 0.1557 T22: 0.1554 REMARK 3 T33: 0.1543 T12: -0.0040 REMARK 3 T13: 0.0070 T23: 0.0215 REMARK 3 L TENSOR REMARK 3 L11: 1.9510 L22: 2.3628 REMARK 3 L33: 1.0751 L12: -1.0153 REMARK 3 L13: 0.4036 L23: 0.0038 REMARK 3 S TENSOR REMARK 3 S11: -0.1046 S12: -0.0879 S13: -0.0711 REMARK 3 S21: 0.1832 S22: 0.1056 S23: 0.2087 REMARK 3 S31: -0.0159 S32: -0.0594 S33: 0.0158 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 6A4X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1300008160. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-APR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 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) : 0.97916 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 : TRUNCATE REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18139 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.630 REMARK 200 RESOLUTION RANGE LOW (A) : 40.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.63 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.90700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: 6A4Z REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM ACETATE, SODIUM CITRATE REMARK 280 TRIBASIC DIHYDRATE, PEG 4000, PH 5.6, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 295.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 23.58500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 38.43500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 38.43500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 11.79250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 38.43500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 38.43500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.37750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 38.43500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.43500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 11.79250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 38.43500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.43500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 35.37750 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 23.58500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 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 427 O HOH A 472 1.93 REMARK 500 O HOH A 453 O HOH A 469 1.93 REMARK 500 O HOH A 334 O HOH A 422 1.99 REMARK 500 NH2 ARG A 54 O HOH A 301 2.00 REMARK 500 OE2 GLU A 29 O HOH A 302 2.01 REMARK 500 NH2 ARG A 20 O HOH A 303 2.04 REMARK 500 OE1 GLU A 80 O HOH A 304 2.15 REMARK 500 O HOH A 412 O HOH A 434 2.19 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 THR A 2 28.70 -69.18 REMARK 500 SER A 125 -132.12 -101.87 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 FE2 A 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 7 NE2 REMARK 620 2 HIS A 61 NE2 52.5 REMARK 620 3 GLU A 117 OE1 47.4 5.3 REMARK 620 4 TYR A 123 OH 48.7 7.9 5.5 REMARK 620 5 HOH A 307 O 52.8 4.0 5.9 5.1 REMARK 620 6 HOH A 404 O 55.9 8.2 10.3 7.2 4.6 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE2 A 201 DBREF1 6A4X A 1 127 UNP A0A124H109_9ACTN DBREF2 6A4X A A0A124H109 1 127 SEQADV 6A4X GLY A -2 UNP A0A124H10 EXPRESSION TAG SEQADV 6A4X SER A -1 UNP A0A124H10 EXPRESSION TAG SEQADV 6A4X HIS A 0 UNP A0A124H10 EXPRESSION TAG SEQRES 1 A 130 GLY SER HIS MET THR VAL GLN LEU ASN HIS THR ILE VAL SEQRES 2 A 130 ALA ALA HIS ASP LYS LYS ALA SER ALA ARG PHE LEU ALA SEQRES 3 A 130 ASP ILE LEU GLY LEU GLU VAL SER PRO GLN TYR GLY PRO SEQRES 4 A 130 PHE ILE PRO VAL GLU ILE PRO ASN GLY VAL SER LEU ASP SEQRES 5 A 130 TYR LEU ASP SER ARG GLY ALA ILE THR PRO GLN HIS TYR SEQRES 6 A 130 ALA PHE LEU VAL SER GLU ASP ASP PHE ASP THR ILE PHE SEQRES 7 A 130 GLY ARG ILE ARG GLU ALA GLY LEU THR TYR TRP ALA ASP SEQRES 8 A 130 PRO TYR HIS ARG ARG PRO GLY GLU ILE ASN HIS ASN ASP SEQRES 9 A 130 GLY GLY ARG GLY ALA TYR PHE GLU ASP PRO ASN GLY HIS SEQRES 10 A 130 ASN LEU GLU ILE LEU THR ARG PRO TYR GLY SER GLY GLY HET FE2 A 201 1 HETNAM FE2 FE (II) ION FORMUL 2 FE2 FE 2+ FORMUL 3 HOH *175(H2 O) HELIX 1 AA1 ASP A 14 GLY A 27 1 14 HELIX 2 AA2 SER A 67 ALA A 81 1 15 HELIX 3 AA3 HIS A 99 GLY A 103 5 5 SHEET 1 AA1 3 HIS A 7 ALA A 12 0 SHEET 2 AA1 3 VAL A 46 ASP A 52 1 O ASP A 49 N THR A 8 SHEET 3 AA1 3 PHE A 37 ILE A 42 -1 N ILE A 42 O VAL A 46 SHEET 1 AA2 3 HIS A 61 LEU A 65 0 SHEET 2 AA2 3 ASN A 115 LEU A 119 1 O GLU A 117 N PHE A 64 SHEET 3 AA2 3 GLY A 105 GLU A 109 -1 N PHE A 108 O LEU A 116 LINK NE2 HIS A 7 FE FE2 A 201 1555 7555 2.39 LINK NE2 HIS A 61 FE FE2 A 201 1555 1555 2.35 LINK OE1 GLU A 117 FE FE2 A 201 1555 1555 1.99 LINK OH TYR A 123 FE FE2 A 201 1555 1555 2.43 LINK FE FE2 A 201 O HOH A 307 1555 1555 2.09 LINK FE FE2 A 201 O HOH A 404 1555 7555 2.26 SITE 1 AC1 6 HIS A 7 HIS A 61 GLU A 117 TYR A 123 SITE 2 AC1 6 HOH A 307 HOH A 404 CRYST1 76.870 76.870 47.170 90.00 90.00 90.00 P 41 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 0.013009 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013009 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021200 0.00000