HEADER METAL TRANSPORT 18-APR-11 2YGJ TITLE METHANOBACTIN MB4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHANOBACTIN MB4; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHYLOCYSTIS SP.; SOURCE 3 ORGANISM_TAXID: 51782; SOURCE 4 STRAIN: M KEYWDS METAL TRANSPORT, METHANOTROPHS EXPDTA X-RAY DIFFRACTION AUTHOR A.GHAZOUANI,A.BASLE,S.J.FIRBANK,J.GRAY,C.DENNISON REVDAT 4 22-MAY-19 2YGJ 1 REMARK LINK REVDAT 3 03-OCT-12 2YGJ 1 JRNL REVDAT 2 23-MAY-12 2YGJ 1 JRNL REVDAT 1 25-APR-12 2YGJ 0 JRNL AUTH A.EL GHAZOUANI,A.BASLE,J.GRAY,D.W.GRAHAM,S.J.FIRBANK, JRNL AUTH 2 C.DENNISON JRNL TITL VARIATIONS IN METHANOBACTIN STRUCTURE INFLUENCES COPPER JRNL TITL 2 UTILIZATION BY METHANE-OXIDIZING BACTERIA. JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 8400 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 22582172 JRNL DOI 10.1073/PNAS.1112921109 REMARK 2 REMARK 2 RESOLUTION. 0.80 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) : 0.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 79.0 REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.087 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.086 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.109 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 210 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 4446 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.075 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.096 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.075 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 192 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 3987 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 59 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 13 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 73.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 35.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 3 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 708 REMARK 3 NUMBER OF RESTRAINTS : 667 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 ANGLE DISTANCES (A) : 0.000 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.000 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.000 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.004 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.015 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.042 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER 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 2YGJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-APR-11. REMARK 100 THE DEPOSITION ID IS D_1290048029. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-FEB-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8 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 : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4702 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.800 REMARK 200 RESOLUTION RANGE LOW (A) : 14.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 78.3 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 27.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.45000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXCDE REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 15.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5, 4.3M NACL. 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 4.53000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.32500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 6.66000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 21.32500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 4.53000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 6.66000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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: 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 SER A 3 N - CA - CB ANGL. DEV. = -9.1 DEGREES 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 SER A 3 45.44 -140.28 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 A1007 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HM9 A 1 SAE REMARK 620 2 HM9 A 1 NAB 87.5 REMARK 620 3 HM8 A 4 NBA 107.9 122.2 REMARK 620 4 HM8 A 4 SBG 120.8 131.2 88.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1009 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HM8 A 4 OBZ REMARK 620 2 HOH A2009 O 99.2 REMARK 620 3 MET A 6 O 95.3 163.9 REMARK 620 4 HOH A2010 O 74.0 89.9 87.4 REMARK 620 5 HOH A2013 O 146.9 92.2 71.8 75.0 REMARK 620 6 HOH A2012 O 99.9 100.6 83.7 168.7 108.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1008 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HM8 A 4 OBY REMARK 620 2 HOH A2004 O 76.9 REMARK 620 3 HOH A2002 O 75.7 10.5 REMARK 620 4 HOH A2011 O 68.2 13.3 7.5 REMARK 620 5 HOH A2010 O 72.8 4.2 10.0 10.3 REMARK 620 6 HM8 A 4 OBY 64.3 15.1 11.5 4.2 11.4 REMARK 620 7 MET A 6 O 65.8 11.4 16.2 12.7 7.8 10.9 REMARK 620 N 1 2 3 4 5 6 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 1007 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1008 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1009 DBREF 2YGJ A 1 6 PDB 2YGJ 2YGJ 1 6 SEQRES 1 A 6 HM9 ALA SER HM8 ALA MET HET HM9 A 1 17 HET HM8 A 4 17 HET CU A1007 1 HET NA A1008 1 HET NA A1009 1 HETNAM HM9 6-(3-CARBAMIMIDAMIDOPROPYL)-3,5-DIHYDROXYPYRAZINE-2- HETNAM 2 HM9 CARBOTHIOIC S-ACID HETNAM HM8 2-[(1S,2R)-1-AMINO-2-(SULFOOXY)PROPYL]-5-HYDROXY-1,3- HETNAM 2 HM8 OXAZOLE-4-CARBOTHIOIC O-ACID HETNAM CU COPPER (II) ION HETNAM NA SODIUM ION FORMUL 1 HM9 C9 H13 N5 O3 S FORMUL 1 HM8 C7 H10 N2 O7 S2 FORMUL 2 CU CU 2+ FORMUL 3 NA 2(NA 1+) FORMUL 5 HOH *13(H2 O) LINK C HM9 A 1 N ALA A 2 1555 1555 1.33 LINK SAE HM9 A 1 CU CU A1007 1555 1555 2.27 LINK NAB HM9 A 1 CU CU A1007 1555 1555 2.03 LINK C SER A 3 N HM8 A 4 1555 1555 1.36 LINK OBZ HM8 A 4 NA NA A1009 1555 1555 2.69 LINK OBY HM8 A 4 NA NA A1008 1555 3345 2.41 LINK NBA HM8 A 4 CU CU A1007 1555 1555 2.03 LINK C HM8 A 4 N ALA A 5 1555 1555 1.35 LINK SBG HM8 A 4 CU CU A1007 1555 1555 2.27 LINK NA NA A1008 O HOH A2004 1555 3345 2.42 LINK NA NA A1008 O HOH A2002 1555 1455 2.33 LINK NA NA A1008 O HOH A2011 1555 1555 2.39 LINK NA NA A1008 O HOH A2010 1555 3355 2.41 LINK NA NA A1008 OBY HM8 A 4 1555 3355 2.41 LINK NA NA A1008 O MET A 6 1555 1555 2.35 LINK NA NA A1009 O HOH A2009 1555 4445 2.21 LINK NA NA A1009 O MET A 6 1555 3345 2.39 LINK NA NA A1009 O HOH A2010 1555 1555 2.39 LINK NA NA A1009 O HOH A2013 1555 1555 2.67 LINK NA NA A1009 O HOH A2012 1555 3345 2.28 SITE 1 AC1 2 HM9 A 1 HM8 A 4 SITE 1 AC2 7 HM8 A 4 MET A 6 NA A1009 HOH A2002 SITE 2 AC2 7 HOH A2004 HOH A2010 HOH A2011 SITE 1 AC3 7 HM8 A 4 MET A 6 NA A1008 HOH A2009 SITE 2 AC3 7 HOH A2010 HOH A2012 HOH A2013 CRYST1 9.060 13.320 42.650 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 0.110375 0.000000 0.000000 0.00000 SCALE2 0.000000 0.075075 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023447 0.00000 MASTER 262 0 5 0 0 0 5 6 0 0 0 1 END