HEADER OXIDOREDUCTASE 29-JUN-04 1TVC TITLE FAD AND NADH BINDING DOMAIN OF METHANE MONOOXYGENASE REDUCTASE FROM TITLE 2 METHYLOCOCCUS CAPSULATUS (BATH) COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHANE MONOOXYGENASE COMPONENT C; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN; COMPND 5 SYNONYM: METHANE HYDROXYLASE; METHANE MONOOXYGENASE REDUCTASE; MMOR; COMPND 6 EC: 1.14.13.25; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHYLOCOCCUS CAPSULATUS; SOURCE 3 ORGANISM_TAXID: 414; SOURCE 4 GENE: MMOC; 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_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PFAD21 KEYWDS FAD-BINDING; NADH-BINDING, OXIDOREDUCTASE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR L.L.CHATWOOD,J.MUELLER,J.D.GROSS,G.WAGNER,S.J.LIPPARD REVDAT 3 02-MAR-22 1TVC 1 REMARK REVDAT 2 24-FEB-09 1TVC 1 VERSN REVDAT 1 12-OCT-04 1TVC 0 JRNL AUTH L.L.CHATWOOD,J.D.GROSS,G.WAGNER,S.J.LIPPARD JRNL TITL NMR STRUCTURE OF THE FLAVIN DOMAIN FROM SOLUBLE METHANE JRNL TITL 2 MONOOXYGENASE REDUCTASE FROM METHYLOCOCCUS CAPSULATUS (BATH) JRNL REF BIOCHEMISTRY V. 43 11983 2004 JRNL REFN ISSN 0006-2960 JRNL PMID 15379538 JRNL DOI 10.1021/BI049066N REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.5, X-PLOR 3.84 REMARK 3 AUTHORS : BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1TVC COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUL-04. REMARK 100 THE DEPOSITION ID IS D_1000022937. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 50MM NA PHOSPHATE REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.6-1MM PROTEIN; 50MM PHOSPHATE REMARK 210 BUFFER; 1MM DTT, 2MM PROTEASE REMARK 210 INHIBITOR; 0.1% NAN3; 3MM NADH; REMARK 210 30MM DITHIONITE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : A STANDARD SET OF NMR REMARK 210 EXPERIMENTS REQUIRED FOR HIGH- REMARK 210 RESOLUTION STRUCTURE; TROSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : DRX; UNITY INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 97.0, DYANA 1.5, PROSA REMARK 210 6.0, VNMR 5.1A, XEASY 1.3.13 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 H VAL A 183 O GLU A 193 1.46 REMARK 500 O GLY A 218 H PHE A 245 1.46 REMARK 500 O LYS A 114 HH TYR A 215 1.48 REMARK 500 O GLU A 46 H GLY A 48 1.52 REMARK 500 OG1 THR A 58 H ASP A 59 1.53 REMARK 500 O GLY A 106 H LEU A 108 1.54 REMARK 500 O GLU A 158 H LEU A 161 1.58 REMARK 500 O LEU A 130 H VAL A 134 1.60 REMARK 500 REMARK 500 REMARK: NULL 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 6 ILE A 55 N ILE A 55 CA 6.225 REMARK 500 6 ILE A 55 CA ILE A 55 CB 8.484 REMARK 500 6 ILE A 55 CA ILE A 55 C 6.777 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 6 ILE A 55 C - N - CA ANGL. DEV. = 110.6 DEGREES REMARK 500 6 ILE A 55 CB - CA - C ANGL. DEV. = -99.8 DEGREES REMARK 500 6 ILE A 55 N - CA - CB ANGL. DEV. = 105.5 DEGREES REMARK 500 6 ILE A 55 CA - CB - CG2 ANGL. DEV. = 13.1 DEGREES REMARK 500 6 ILE A 55 N - CA - C ANGL. DEV. = -93.9 DEGREES REMARK 500 6 ILE A 55 CA - C - O ANGL. DEV. = -51.3 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 1 SER A 5 110.96 -161.28 REMARK 500 1 PHE A 6 71.08 -168.12 REMARK 500 1 LEU A 19 71.63 87.87 REMARK 500 1 LYS A 33 -0.32 -149.22 REMARK 500 1 ASP A 36 -34.68 155.03 REMARK 500 1 GLU A 37 59.91 -169.87 REMARK 500 1 CYS A 38 -65.91 -164.07 REMARK 500 1 LYS A 44 26.65 -163.07 REMARK 500 1 PHE A 45 96.61 76.55 REMARK 500 1 PRO A 47 59.12 -61.59 REMARK 500 1 GLN A 49 146.21 -35.44 REMARK 500 1 ILE A 55 -70.95 -34.49 REMARK 500 1 THR A 58 -103.18 -40.69 REMARK 500 1 ASP A 59 36.16 160.23 REMARK 500 1 VAL A 60 27.24 -152.32 REMARK 500 1 SER A 61 -101.87 -97.46 REMARK 500 1 ARG A 62 -176.63 170.64 REMARK 500 1 ASN A 68 -69.76 -105.35 REMARK 500 1 LEU A 69 160.27 138.30 REMARK 500 1 PRO A 70 87.75 -60.93 REMARK 500 1 ASN A 71 117.65 -168.08 REMARK 500 1 PRO A 72 89.95 -68.13 REMARK 500 1 GLU A 73 -82.87 -158.09 REMARK 500 1 GLU A 85 5.29 84.47 REMARK 500 1 ASP A 95 13.58 -151.56 REMARK 500 1 ARG A 97 -171.98 -56.81 REMARK 500 1 PRO A 107 60.74 -65.37 REMARK 500 1 TRP A 143 -84.34 -80.54 REMARK 500 1 THR A 144 23.66 -156.60 REMARK 500 1 ASN A 147 -159.93 -69.97 REMARK 500 1 VAL A 155 -116.25 -164.15 REMARK 500 1 ASN A 156 -164.27 -119.91 REMARK 500 1 THR A 157 -41.38 -25.95 REMARK 500 1 GLU A 158 -43.27 107.82 REMARK 500 1 LEU A 161 -165.69 -110.58 REMARK 500 1 PHE A 162 -154.59 178.26 REMARK 500 1 SER A 173 -71.06 -61.48 REMARK 500 1 MET A 174 -153.54 -179.92 REMARK 500 1 ARG A 175 95.42 42.59 REMARK 500 1 ASN A 176 73.69 -13.45 REMARK 500 1 VAL A 183 146.66 56.23 REMARK 500 1 TRP A 184 -63.40 -133.30 REMARK 500 1 HIS A 185 51.47 -168.65 REMARK 500 1 PRO A 186 -101.72 -88.01 REMARK 500 1 SER A 187 -8.01 153.23 REMARK 500 1 GLU A 193 -85.30 -167.09 REMARK 500 1 SER A 196 166.01 146.25 REMARK 500 1 PRO A 197 44.33 -81.93 REMARK 500 1 SER A 207 -87.96 -92.11 REMARK 500 1 SER A 208 103.71 163.28 REMARK 500 REMARK 500 THIS ENTRY HAS 556 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 THR A 54 ILE A 55 6 -71.01 REMARK 500 ILE A 55 PRO A 56 6 72.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 6 ILE A 55 -30.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FDA A 252 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JQ4 RELATED DB: PDB REMARK 900 [2FE-2S] FERREDOXIN DOMAIN OF METHANE MONOOXYGENASE REDUCTASE DBREF 1TVC A 2 251 UNP P22868 MMOC_METCA 99 348 SEQRES 1 A 250 CYS ARG ILE SER PHE GLY GLU VAL GLY SER PHE GLU ALA SEQRES 2 A 250 GLU VAL VAL GLY LEU ASN TRP VAL SER SER ASN THR VAL SEQRES 3 A 250 GLN PHE LEU LEU GLN LYS ARG PRO ASP GLU CYS GLY ASN SEQRES 4 A 250 ARG GLY VAL LYS PHE GLU PRO GLY GLN PHE MET ASP LEU SEQRES 5 A 250 THR ILE PRO GLY THR ASP VAL SER ARG SER TYR SER PRO SEQRES 6 A 250 ALA ASN LEU PRO ASN PRO GLU GLY ARG LEU GLU PHE LEU SEQRES 7 A 250 ILE ARG VAL LEU PRO GLU GLY ARG PHE SER ASP TYR LEU SEQRES 8 A 250 ARG ASN ASP ALA ARG VAL GLY GLN VAL LEU SER VAL LYS SEQRES 9 A 250 GLY PRO LEU GLY VAL PHE GLY LEU LYS GLU ARG GLY MET SEQRES 10 A 250 ALA PRO ARG TYR PHE VAL ALA GLY GLY THR GLY LEU ALA SEQRES 11 A 250 PRO VAL VAL SER MET VAL ARG GLN MET GLN GLU TRP THR SEQRES 12 A 250 ALA PRO ASN GLU THR ARG ILE TYR PHE GLY VAL ASN THR SEQRES 13 A 250 GLU PRO GLU LEU PHE TYR ILE ASP GLU LEU LYS SER LEU SEQRES 14 A 250 GLU ARG SER MET ARG ASN LEU THR VAL LYS ALA CYS VAL SEQRES 15 A 250 TRP HIS PRO SER GLY ASP TRP GLU GLY GLU GLN GLY SER SEQRES 16 A 250 PRO ILE ASP ALA LEU ARG GLU ASP LEU GLU SER SER ASP SEQRES 17 A 250 ALA ASN PRO ASP ILE TYR LEU CYS GLY PRO PRO GLY MET SEQRES 18 A 250 ILE ASP ALA ALA CYS GLU LEU VAL ARG SER ARG GLY ILE SEQRES 19 A 250 PRO GLY GLU GLN VAL PHE PHE GLU LYS PHE LEU PRO SER SEQRES 20 A 250 GLY ALA ALA HET FDA A 252 86 HETNAM FDA DIHYDROFLAVINE-ADENINE DINUCLEOTIDE FORMUL 2 FDA C27 H35 N9 O15 P2 HELIX 1 1 PHE A 88 ALA A 96 1 9 HELIX 2 2 LEU A 130 THR A 144 1 15 HELIX 3 3 TYR A 163 MET A 174 1 12 HELIX 4 4 ILE A 198 SER A 208 1 11 HELIX 5 5 PRO A 219 GLY A 234 1 16 SHEET 1 A 4 SER A 11 GLU A 15 0 SHEET 2 A 4 VAL A 101 LEU A 108 -1 O LEU A 102 N ALA A 14 SHEET 3 A 4 PHE A 50 LEU A 53 -1 N ASP A 52 O LYS A 105 SHEET 4 A 4 ARG A 62 TYR A 64 -1 O ARG A 62 N LEU A 53 SHEET 1 B 3 ASN A 20 SER A 23 0 SHEET 2 B 3 THR A 26 LEU A 31 -1 O GLN A 28 N ASN A 20 SHEET 3 B 3 LEU A 76 ILE A 80 -1 O PHE A 78 N PHE A 29 SHEET 1 C 5 THR A 178 ALA A 181 0 SHEET 2 C 5 THR A 149 GLY A 154 1 N ILE A 151 O THR A 178 SHEET 3 C 5 ARG A 121 GLY A 126 1 N ARG A 121 O ARG A 150 SHEET 4 C 5 ASP A 213 CYS A 217 1 O CYS A 217 N VAL A 124 SHEET 5 C 5 GLN A 239 PHE A 242 1 O PHE A 241 N ILE A 214 SITE 1 AC1 21 ASN A 25 PHE A 50 ARG A 62 SER A 63 SITE 2 AC1 21 TYR A 64 SER A 65 LEU A 79 ILE A 80 SITE 3 AC1 21 ARG A 81 VAL A 82 LEU A 83 PHE A 88 SITE 4 AC1 21 VAL A 110 GLY A 129 ASN A 156 GLU A 160 SITE 5 AC1 21 SER A 187 GLY A 188 GLU A 243 PHE A 245 SITE 6 AC1 21 LEU A 246 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1