HEADER OXIDOREDUCTASE 06-JUL-10 2XJI TITLE STRUCTURE AND COPPER-BINDING PROPERTIES OF METHANOBACTINS FROM TITLE 2 METHYLOSINUS TRICHOSPORIUM OB3B COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHANOBACTIN MB-OB3B; COMPND 3 CHAIN: A, B, C, D, E, F; COMPND 4 SYNONYM: COPPER-BINDING COMPOUND, CBC, HYDROGEN PEROXIDE REDUCTASE, COMPND 5 SUPEROXIDE DISMUTASE, MINUS-MET METHANOBACTIN; COMPND 6 EC: 1.11.1.-, 1.15.1.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHYLOSINUS TRICHOSPORIUM; SOURCE 3 ORGANISM_TAXID: 595536; SOURCE 4 STRAIN: OB3B; SOURCE 5 OTHER_DETAILS: NCIMB 11131 KEYWDS OXIDOREDUCTASE, METAL TRANSPORT, METHANOTROPHS, OXAZALONE EXPDTA X-RAY DIFFRACTION AUTHOR A.EL-GHAZOUANI,A.BASLE,S.J.FIRBANK,C.W.KNAPP,J.GRAY,D.W.GRAHAM, AUTHOR 2 C.DENNISON REVDAT 7 10-JUL-19 2XJI 1 REMARK REVDAT 6 22-MAY-19 2XJI 1 REMARK LINK ATOM REVDAT 5 24-JUL-13 2XJI 1 REMARK HETSYN REVDAT 4 09-MAY-12 2XJI 1 REMARK REVDAT 3 28-MAR-12 2XJI 1 HEADER COMPND KEYWDS REMARK REVDAT 3 2 1 VERSN DBREF SEQRES MODRES REVDAT 3 3 1 HET HETNAM FORMUL LINK REVDAT 3 4 1 SITE HETATM ANISOU ATOM REVDAT 3 5 1 CONECT MASTER REVDAT 2 18-MAY-11 2XJI 1 JRNL REVDAT 1 02-FEB-11 2XJI 0 JRNL AUTH A.EL GHAZOUANI,A.BASLE,S.J.FIRBANK,C.W.KNAPP,J.GRAY, JRNL AUTH 2 D.W.GRAHAM,C.DENNISON JRNL TITL COPPER-BINDING PROPERTIES AND STRUCTURES OF METHANOBACTINS JRNL TITL 2 FROM METHYLOSINUS TRICHOSPORIUM OB3B. JRNL REF INORG.CHEM. V. 50 1378 2011 JRNL REFN ISSN 0020-1669 JRNL PMID 21254756 JRNL DOI 10.1021/IC101965J REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.J.KIM,D.W.GRAHAM,A.A.DISPIRITO,M.A.ALTERMAN,N.GALEVA, REMARK 1 AUTH 2 C.K.LARIVE,D.ASUNSKIS,P.M.A.SHERWOOD REMARK 1 TITL METHANOBACTIN, A COPPER-ACQUISITION COMPOUND FROM REMARK 1 TITL 2 METHANE-OXIDIZING BACTERIA. REMARK 1 REF SCIENCE V. 305 1612 2004 REMARK 1 REFN ISSN 0036-8075 REMARK 1 PMID 15361623 REMARK 1 DOI 10.1126/SCIENCE.1098322 REMARK 1 REFERENCE 2 REMARK 1 AUTH L.A.BEHLING,S.C.HARTSEL,D.E.LEWIS,A.A.DISPIRITO,D.W.CHOI, REMARK 1 AUTH 2 L.R.MASTERSON,G.VEGLIA,W.H.GALLAGHER REMARK 1 TITL NMR, MASS SPECTROMETRY AND CHEMICAL EVIDENCE REVEAL A REMARK 1 TITL 2 DIFFERENT CHEMICAL STRUCTURE FOR METHANOBACTIN THAT CONTAINS REMARK 1 TITL 3 OXAZOLONE RINGS. REMARK 1 REF J.AM.CHEM.SOC. V. 130 12604 2008 REMARK 1 REFN ISSN 0002-7863 REMARK 1 PMID 18729522 REMARK 1 DOI 10.1021/JA804747D REMARK 2 REMARK 2 RESOLUTION. 1.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : THIN SHELL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.114 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.129 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1469 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 27860 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.107 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.120 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1305 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 24631 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 396 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 68 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 471.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 252.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 35 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 5724 REMARK 3 NUMBER OF RESTRAINTS : 8640 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.026 REMARK 3 ANGLE DISTANCES (A) : 0.062 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.024 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.104 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.071 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.037 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.038 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2XJI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-JUL-10. REMARK 100 THE DEPOSITION ID IS D_1290044496. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29329 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.000 REMARK 200 RESOLUTION RANGE LOW (A) : 21.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.36000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 13.50 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: PREVIOUSLY SOLVED MODEL CCDC BIDLOQ WAS MANUALLY FITTED REMARK 200 INTO DENSITY REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M AMMONIUM SULFATE, 5% ISOPROPANOL, REMARK 280 PH 7.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 15.85500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 19.78500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 42.52500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 15.85500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 19.78500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 42.52500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 15.85500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 19.78500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 42.52500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 15.85500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 19.78500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 42.52500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4, 5, 6, 7, 8, 9 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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 REMARK 350 BIOMOLECULE: 5 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E 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 REMARK 350 BIOMOLECULE: 6 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: F 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 REMARK 350 BIOMOLECULE: 7 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 1580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 REMARK 350 BIOMOLECULE: 8 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 1560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 REMARK 350 BIOMOLECULE: 9 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 1430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B2005 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 METHANOBACTIN IS A MEMBER OF THE FAMILY OF CHALKOPHORES, A COPPER REMARK 400 CHELATING AGENT INVOLVED IN SCAVENGING, UPTAKE AND SUPPRESSION OF REMARK 400 TOXICITY OF COPPER. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: METHANOBACTIN REMARK 400 CHAIN: A, B, C, D, E, F REMARK 400 COMPONENT_1: METHANOBACTIN PEPTIDE, RESIDUES 0 TO 10 REMARK 400 COMPONENT_2: COPPER ATOM, RESIDUE 1001 REMARK 400 REMARK 400 DESCRIPTION: METHANOBACTIN IS A COPPER BINDING COMPOUND REMARK 400 HAVING ANTIBIOTIC AND ANTIOXIDANT ACTIVITY ISOLATED FROM REMARK 400 METHANOTROPHIC BACTERIA. METHANOBACTIN MAY FUNCTION IN COPPER REMARK 400 UPTAKE, REGULATION OF METHANE MONOOXYGENASE EXPRESSION, REMARK 400 PROTECTION AGAINST COPPER TOXICITY, AND PARTICULATE METHANE REMARK 400 MONOOXYGENASE ACTIVITY. METHANOBACTIN CAN EXTRACT COPPER FROM REMARK 400 INSOLUBLE MINERALS AND COULD BE IMPORTANT FOR MINERAL WEATHERING. REMARK 400 MANY METHANOBACTIN PROPERTIES ARE REMINISCENT OF IRON SIDEROPHORES REMARK 400 SUGGESTING A SIMILAR MECHANISM OF HANDLING. METHANOBACTIN-LIKE REMARK 400 COMPOUNDS HAVE ALSO BEEN IDENTIFIED IN YEAST MITOCHONDRIA, SUGGEST REMARK 400 THAT THESE MOLECULES ARE A MORE UNIVERSAL PHENOMENON. REMARK 400 REMARK 400 THE METHANOBACTIN IS CHALKOPHORE, POLYPEPTIDE, A MEMBER OF METAL REMARK 400 TRANSPORT CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: METHANOBACTIN REMARK 400 CHAIN: A, B, C, D, E, F REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 COMPONENT_2: RESIDUE CU REMARK 400 DESCRIPTION: NULL 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 100 REMARK 465 MET B 100 REMARK 465 MET C 100 REMARK 465 MET D 100 REMARK 465 MET E 100 REMARK 465 MET F 100 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 PRO B 6 N PRO B 6 CA 0.107 REMARK 500 GLY C 2 CA GLY C 2 C -0.181 REMARK 500 GLY C 2 C GLY C 2 O 0.109 REMARK 500 PRO C 6 N PRO C 6 CA 0.126 REMARK 500 PRO C 6 N PRO C 6 CA 0.123 REMARK 500 PRO D 6 N PRO D 6 CA 0.138 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 BB9 A 7 C - N - CA ANGL. DEV. = -15.3 DEGREES REMARK 500 TYR B 5 CB - CG - CD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 TYR B 5 CB - CG - CD1 ANGL. DEV. = -4.6 DEGREES REMARK 500 GLY C 2 N - CA - C ANGL. DEV. = 17.7 DEGREES REMARK 500 TYR C 5 CB - CG - CD2 ANGL. DEV. = 4.1 DEGREES REMARK 500 PRO C 6 CA - N - CD ANGL. DEV. = 8.9 DEGREES REMARK 500 PRO C 6 N - CA - CB ANGL. DEV. = -7.5 DEGREES REMARK 500 PRO D 6 CA - N - CD ANGL. DEV. = 9.3 DEGREES REMARK 500 PRO D 6 N - CA - CB ANGL. DEV. = -6.7 DEGREES REMARK 500 PRO D 6 N - CD - CG ANGL. DEV. = -8.2 DEGREES REMARK 500 BB9 E 7 C - N - CA ANGL. DEV. = -15.7 DEGREES 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 CU A 11 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 BB9 A 1 SG REMARK 620 2 BB9 A 1 N 86.8 REMARK 620 3 BB9 A 7 N 115.1 128.6 REMARK 620 4 BB9 A 7 SG 110.5 127.9 89.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU B 11 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 BB9 B 1 N REMARK 620 2 BB9 B 1 SG 85.1 REMARK 620 3 BB9 B 7 N 125.0 113.2 REMARK 620 4 BB9 B 7 SG 139.0 104.8 88.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU C 11 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 BB9 C 1 SG REMARK 620 2 BB9 C 1 N 82.5 REMARK 620 3 BB9 C 7 SG 107.3 137.9 REMARK 620 4 BB9 C 7 N 113.8 124.8 89.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU C 11 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 BB9 C 1 SG REMARK 620 2 BB9 C 1 N 86.4 REMARK 620 3 BB9 C 7 SG 102.9 133.3 REMARK 620 4 BB9 C 7 N 119.0 129.4 85.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU D 11 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 BB9 D 1 SG REMARK 620 2 BB9 D 1 N 83.0 REMARK 620 3 BB9 D 7 SG 103.7 124.7 REMARK 620 4 BB9 D 7 N 114.0 142.7 85.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU D 11 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 BB9 D 1 N REMARK 620 2 BB9 D 1 SG 85.6 REMARK 620 3 BB9 D 7 N 130.1 114.7 REMARK 620 4 BB9 D 7 SG 131.7 106.4 87.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU E 11 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 BB9 E 1 N REMARK 620 2 BB9 E 1 SG 86.2 REMARK 620 3 BB9 E 7 N 125.1 112.9 REMARK 620 4 BB9 E 7 SG 137.5 105.3 88.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU F 11 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 BB9 F 1 SG REMARK 620 2 BB9 F 1 N 86.1 REMARK 620 3 BB9 F 7 N 115.8 128.5 REMARK 620 4 BB9 F 7 SG 110.4 129.1 88.3 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 CU A 11 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU B 11 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU C 11 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU D 11 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU E 11 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU F 11 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2XJH RELATED DB: PDB REMARK 900 STRUCTURE AND COPPER-BINDING PROPERTIES OF METHANOBACTINS FROM REMARK 900 METHYLOSINUS TRICHOSPORIUM OB3B DBREF 2XJI A 0 10 UNP E3YBA4 MBCTN_METTR 20 30 DBREF 2XJI B 0 10 UNP E3YBA4 MBCTN_METTR 20 30 DBREF 2XJI C 0 10 UNP E3YBA4 MBCTN_METTR 20 30 DBREF 2XJI D 0 10 UNP E3YBA4 MBCTN_METTR 20 30 DBREF 2XJI E 0 10 UNP E3YBA4 MBCTN_METTR 20 30 DBREF 2XJI F 0 10 UNP E3YBA4 MBCTN_METTR 20 30 SEQRES 1 A 11 COI BB9 GLY SER CYS TYR PRO BB9 SER CYS MET SEQRES 1 B 11 COI BB9 GLY SER CYS TYR PRO BB9 SER CYS MET SEQRES 1 C 11 COI BB9 GLY SER CYS TYR PRO BB9 SER CYS MET SEQRES 1 D 11 COI BB9 GLY SER CYS TYR PRO BB9 SER CYS MET SEQRES 1 E 11 COI BB9 GLY SER CYS TYR PRO BB9 SER CYS MET SEQRES 1 F 11 COI BB9 GLY SER CYS TYR PRO BB9 SER CYS MET MODRES 2XJI BB9 A 1 CYS MODRES 2XJI BB9 A 7 CYS MODRES 2XJI BB9 B 1 CYS MODRES 2XJI BB9 B 7 CYS MODRES 2XJI BB9 C 1 CYS MODRES 2XJI BB9 C 7 CYS MODRES 2XJI BB9 D 1 CYS MODRES 2XJI BB9 D 7 CYS MODRES 2XJI BB9 E 1 CYS MODRES 2XJI BB9 E 7 CYS MODRES 2XJI BB9 F 1 CYS MODRES 2XJI BB9 F 7 CYS HET COI A 0 12 HET BB9 A 1 6 HET BB9 A 7 6 HET COI B 0 8 HET BB9 B 1 6 HET BB9 B 7 6 HET COI C 0 16 HET BB9 C 1 12 HET BB9 C 7 12 HET COI D 0 16 HET BB9 D 1 12 HET BB9 D 7 12 HET COI E 0 8 HET BB9 E 1 6 HET BB9 E 7 6 HET COI F 0 8 HET BB9 F 1 6 HET BB9 F 7 6 HET CU A 11 1 HET CU B 11 1 HET CU C 11 2 HET CU D 11 2 HET CU E 11 1 HET CU F 11 1 HETNAM COI 2-OXO-4-METHYLPENTANOIC ACID HETNAM BB9 (2Z)-2-AMINO-3-SULFANYLPROP-2-ENOIC ACID HETNAM CU COPPER (II) ION HETSYN COI ALPHA-KETOISOCAPROIC ACID FORMUL 1 COI 6(C6 H10 O3) FORMUL 1 BB9 12(C3 H5 N O2 S) FORMUL 7 CU 6(CU 2+) FORMUL 13 HOH *68(H2 O) SSBOND 1 CYS A 4 CYS A 9 1555 1555 2.06 SSBOND 2 CYS B 4 CYS B 9 1555 1555 2.04 SSBOND 3 CYS C 4 CYS C 9 1555 1555 2.05 SSBOND 4 CYS D 4 CYS D 9 1555 1555 2.06 SSBOND 5 CYS E 4 CYS E 9 1555 1555 2.05 SSBOND 6 CYS F 4 CYS F 9 1555 1555 2.04 LINK O2 COI A 0 C BB9 A 1 1555 1555 1.40 LINK C1 COI A 0 N BB9 A 1 1555 1555 1.30 LINK SG BB9 A 1 CU CU A 11 1555 1555 2.37 LINK N BB9 A 1 CU CU A 11 1555 1555 1.98 LINK CB BB9 A 1 N GLY A 2 1555 1555 1.34 LINK CB BB9 A 7 N SER A 8 1555 1555 1.35 LINK N BB9 A 7 CU CU A 11 1555 1555 2.01 LINK N BB9 A 7 C PRO A 6 1555 1555 1.35 LINK SG BB9 A 7 CU CU A 11 1555 1555 2.32 LINK O2 COI B 0 C BB9 B 1 1555 1555 1.36 LINK C1 COI B 0 N BB9 B 1 1555 1555 1.31 LINK N BB9 B 1 CU CU B 11 1555 1555 1.96 LINK CB BB9 B 1 N GLY B 2 1555 1555 1.37 LINK SG BB9 B 1 CU CU B 11 1555 1555 2.45 LINK N BB9 B 7 C PRO B 6 1555 1555 1.32 LINK N BB9 B 7 CU CU B 11 1555 1555 2.01 LINK CB BB9 B 7 N SER B 8 1555 1555 1.35 LINK SG BB9 B 7 CU CU B 11 1555 1555 2.33 LINK O2 BCOI C 0 C BBB9 C 1 1555 1555 1.39 LINK C1 BCOI C 0 N BBB9 C 1 1555 1555 1.31 LINK O2 ACOI C 0 C ABB9 C 1 1555 1555 1.39 LINK C1 ACOI C 0 N ABB9 C 1 1555 1555 1.32 LINK CB ABB9 C 1 N AGLY C 2 1555 1555 1.36 LINK SG ABB9 C 1 CU A CU C 11 1555 1555 2.46 LINK N ABB9 C 1 CU A CU C 11 1555 1555 2.03 LINK CB BBB9 C 1 N BGLY C 2 1555 1555 1.30 LINK SG BBB9 C 1 CU B CU C 11 1555 1555 2.40 LINK N BBB9 C 1 CU B CU C 11 1555 1555 1.86 LINK CB ABB9 C 7 N ASER C 8 1555 1555 1.35 LINK N ABB9 C 7 C APRO C 6 1555 1555 1.33 LINK SG BBB9 C 7 CU B CU C 11 1555 1555 2.39 LINK N BBB9 C 7 CU B CU C 11 1555 1555 2.07 LINK N BBB9 C 7 C BPRO C 6 1555 1555 1.33 LINK CB BBB9 C 7 N BSER C 8 1555 1555 1.35 LINK SG ABB9 C 7 CU A CU C 11 1555 1555 2.28 LINK N ABB9 C 7 CU A CU C 11 1555 1555 2.01 LINK C1 ACOI D 0 N ABB9 D 1 1555 1555 1.30 LINK O2 ACOI D 0 C ABB9 D 1 1555 1555 1.40 LINK C1 BCOI D 0 N BBB9 D 1 1555 1555 1.31 LINK O2 BCOI D 0 C BBB9 D 1 1555 1555 1.37 LINK SG BBB9 D 1 CU B CU D 11 1555 1555 2.44 LINK N BBB9 D 1 CU B CU D 11 1555 1555 1.90 LINK N ABB9 D 1 CU A CU D 11 1555 1555 1.94 LINK CB ABB9 D 1 N AGLY D 2 1555 1555 1.35 LINK SG ABB9 D 1 CU A CU D 11 1555 1555 2.42 LINK CB BBB9 D 1 N BGLY D 2 1555 1555 1.42 LINK CB ABB9 D 7 N ASER D 8 1555 1555 1.33 LINK N BBB9 D 7 C BPRO D 6 1555 1555 1.34 LINK SG BBB9 D 7 CU B CU D 11 1555 1555 2.40 LINK CB BBB9 D 7 N BSER D 8 1555 1555 1.33 LINK N ABB9 D 7 CU A CU D 11 1555 1555 2.03 LINK N ABB9 D 7 C APRO D 6 1555 1555 1.31 LINK SG ABB9 D 7 CU A CU D 11 1555 1555 2.33 LINK N BBB9 D 7 CU B CU D 11 1555 1555 1.95 LINK C1 COI E 0 N BB9 E 1 1555 1555 1.30 LINK O2 COI E 0 C BB9 E 1 1555 1555 1.39 LINK CB BB9 E 1 N GLY E 2 1555 1555 1.35 LINK N BB9 E 1 CU CU E 11 1555 1555 1.98 LINK SG BB9 E 1 CU CU E 11 1555 1555 2.42 LINK N BB9 E 7 CU CU E 11 1555 1555 2.03 LINK CB BB9 E 7 N SER E 8 1555 1555 1.34 LINK N BB9 E 7 C PRO E 6 1555 1555 1.33 LINK SG BB9 E 7 CU CU E 11 1555 1555 2.35 LINK C1 COI F 0 N BB9 F 1 1555 1555 1.31 LINK O2 COI F 0 C BB9 F 1 1555 1555 1.41 LINK SG BB9 F 1 CU CU F 11 1555 1555 2.39 LINK N BB9 F 1 CU CU F 11 1555 1555 1.97 LINK CB BB9 F 1 N GLY F 2 1555 1555 1.33 LINK CB BB9 F 7 N SER F 8 1555 1555 1.33 LINK N BB9 F 7 C PRO F 6 1555 1555 1.33 LINK N BB9 F 7 CU CU F 11 1555 1555 2.05 LINK SG BB9 F 7 CU CU F 11 1555 1555 2.33 CISPEP 1 TYR A 5 PRO A 6 0 -4.01 CISPEP 2 TYR B 5 PRO B 6 0 -13.88 CISPEP 3 TYR B 5 PRO B 6 0 -7.82 CISPEP 4 TYR C 5 PRO C 6 0 -6.42 CISPEP 5 TYR C 5 PRO C 6 0 -5.69 CISPEP 6 TYR D 5 PRO D 6 0 -4.77 CISPEP 7 TYR D 5 PRO D 6 0 -2.47 CISPEP 8 TYR E 5 PRO E 6 0 -8.60 CISPEP 9 TYR F 5 PRO F 6 0 -9.68 SITE 1 AC1 4 COI A 0 BB9 A 1 PRO A 6 BB9 A 7 SITE 1 AC2 4 COI B 0 BB9 B 1 PRO B 6 BB9 B 7 SITE 1 AC3 4 COI C 0 BB9 C 1 PRO C 6 BB9 C 7 SITE 1 AC4 4 COI D 0 BB9 D 1 PRO D 6 BB9 D 7 SITE 1 AC5 4 COI E 0 BB9 E 1 PRO E 6 BB9 E 7 SITE 1 AC6 4 COI F 0 BB9 F 1 PRO F 6 BB9 F 7 CRYST1 31.710 39.570 85.050 90.00 90.00 90.00 I 2 2 2 48 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 0.031536 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025272 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011758 0.00000 HETATM 1 C1 COI A 0 13.441 12.335 4.718 1.00 7.49 C ANISOU 1 C1 COI A 0 1272 1138 436 -183 230 -20 C HETATM 2 O2 COI A 0 12.395 12.101 5.594 1.00 7.74 O ANISOU 2 O2 COI A 0 1144 1334 463 -224 220 -116 O HETATM 3 C2 COI A 0 13.090 12.634 3.286 1.00 8.65 C ANISOU 3 C2 COI A 0 1390 1432 465 -55 175 -108 C HETATM 4 O3 COI A 0 11.865 12.579 2.967 1.00 10.36 O ANISOU 4 O3 COI A 0 1353 1993 589 84 157 -33 O HETATM 5 C3 ACOI A 0 14.112 13.063 2.243 0.43 9.41 C ANISOU 5 C3 ACOI A 0 1654 1678 242 -483 245 -496 C HETATM 6 C3 BCOI A 0 14.314 12.905 2.455 0.57 12.11 C ANISOU 6 C3 BCOI A 0 1654 2232 714 -794 183 406 C HETATM 7 C4 ACOI A 0 13.826 14.518 1.888 0.43 11.77 C ANISOU 7 C4 ACOI A 0 1949 1597 927 -661 709 -298 C HETATM 8 C4 BCOI A 0 14.082 13.315 1.010 0.57 11.11 C ANISOU 8 C4 BCOI A 0 1444 2180 596 -687 247 99 C HETATM 9 C5 ACOI A 0 13.234 15.437 2.943 0.43 15.49 C ANISOU 9 C5 ACOI A 0 3785 1161 939 -699 794 -373 C HETATM 10 C5 BCOI A 0 13.025 14.346 0.761 0.57 19.73 C ANISOU 10 C5 BCOI A 0 3304 2047 2148 -61 215 1183 C HETATM 11 C6 ACOI A 0 13.141 14.678 0.542 0.43 19.26 C ANISOU 11 C6 ACOI A 0 4748 2061 508 195 565 202 C HETATM 12 C6 BCOI A 0 14.208 12.128 0.074 0.57 37.21 C ANISOU 12 C6 BCOI A 0 9453 3346 1339 1850 -529 -700 C HETATM 13 N BB9 A 1 14.631 12.278 5.243 1.00 6.96 N ANISOU 13 N BB9 A 1 1227 953 466 -208 266 71 N HETATM 14 CA BB9 A 1 14.389 11.957 6.572 1.00 7.41 C ANISOU 14 CA BB9 A 1 1176 1119 522 -206 159 -36 C HETATM 15 C BB9 A 1 13.028 11.865 6.814 1.00 6.95 C ANISOU 15 C BB9 A 1 1298 962 380 -242 205 -6 C HETATM 16 O BB9 A 1 12.314 11.647 7.784 1.00 7.97 O ANISOU 16 O BB9 A 1 1268 1165 594 -164 261 -41 O HETATM 17 CB BB9 A 1 15.443 11.752 7.481 1.00 7.05 C ANISOU 17 CB BB9 A 1 1230 848 601 -245 160 114 C HETATM 18 SG BB9 A 1 17.057 11.928 6.979 1.00 7.98 S ANISOU 18 SG BB9 A 1 1191 1139 703 -331 105 85 S