HEADER OXIDOREDUCTASE 30-JUN-09 2KLA TITLE NMR STRUCTURE OF A PUTATIVE DINITROGENASE (MJ0327) FROM METHANOCOCCUS TITLE 2 JANNASCHII COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN MJ0327; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_TAXID: 2190; SOURCE 4 GENE: MJ0327; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET28B KEYWDS PUTATIVE DINITROGENASE, STRUCTURAL GENOMICS, JOINT CENTER FOR KEYWDS 2 STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-2, KEYWDS 3 OXIDOREDUCTASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.JAUDZEMS,B.MOHANTY,M.GERALT,P.SERRANO,I.WILSON,K.WUTHRICH,JOINT AUTHOR 2 CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 6 08-MAY-24 2KLA 1 REMARK REVDAT 5 01-FEB-23 2KLA 1 SEQADV REVDAT 4 26-FEB-20 2KLA 1 REMARK REVDAT 3 23-MAR-11 2KLA 1 JRNL REVDAT 2 28-JUL-10 2KLA 1 HEADER TITLE KEYWDS REVDAT 1 11-AUG-09 2KLA 0 JRNL AUTH K.JAUDZEMS,M.GERALT,P.SERRANO,B.MOHANTY,R.HORST,B.PEDRINI, JRNL AUTH 2 M.A.ELSLIGER,I.A.WILSON,K.WUTHRICH JRNL TITL NMR STRUCTURE OF THE PROTEIN NP_247299.1: COMPARISON WITH JRNL TITL 2 THE CRYSTAL STRUCTURE. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 66 1367 2010 JRNL REFN ESSN 1744-3091 JRNL PMID 20944234 JRNL DOI 10.1107/S1744309110005890 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 3.0, OPAL REMARK 3 AUTHORS : P.GUNTERT ET AL. (CYANA), LUGINBUHL, GUNTERT, REMARK 3 BILLETER AND WUTHRICH (OPAL) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KLA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000101261. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 313 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.029 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 20 MM SODIUM PHOSPHATE, 1 MM REMARK 210 DTT, 0.03 % SODIUM AZIDE, 95% REMARK 210 H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D [15N,1H]-HSQC; 5D APSY REMARK 210 -HACACONH; 4D APSY-HACANH; 5D REMARK 210 APSY-CBCACONH; 3D 15N-RESOLVED REMARK 210 [1H,1H]-NOESY; 3D 13C(ALIPHATIC)- REMARK 210 RESOLVED [1H,1H]-NOESY; 3D REMARK 210 13C(AROMATIC)-RESOLVED [1H,1H]- REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, MOLMOL, UNIO 1.0.2, REMARK 210 CARA 1.8.4 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 80 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: 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 4 VAL A 6 CG1 - CB - CG2 ANGL. DEV. = -11.2 DEGREES REMARK 500 4 VAL A 40 CB - CA - C ANGL. DEV. = 11.9 DEGREES REMARK 500 4 VAL A 40 CG1 - CB - CG2 ANGL. DEV. = -12.1 DEGREES REMARK 500 4 VAL A 40 CA - CB - CG1 ANGL. DEV. = 12.9 DEGREES REMARK 500 6 VAL A 40 CA - CB - CG1 ANGL. DEV. = 13.6 DEGREES REMARK 500 7 VAL A 40 CA - CB - CG1 ANGL. DEV. = 13.2 DEGREES REMARK 500 8 VAL A 40 CB - CA - C ANGL. DEV. = 13.0 DEGREES REMARK 500 8 VAL A 40 CA - CB - CG1 ANGL. DEV. = 9.1 DEGREES REMARK 500 12 VAL A 40 CB - CA - C ANGL. DEV. = 12.0 DEGREES REMARK 500 13 VAL A 40 CB - CA - C ANGL. DEV. = 12.8 DEGREES REMARK 500 13 VAL A 40 CA - CB - CG1 ANGL. DEV. = 9.1 DEGREES REMARK 500 14 LEU A 98 CD1 - CG - CD2 ANGL. DEV. = 20.7 DEGREES REMARK 500 15 LEU A 98 CD1 - CG - CD2 ANGL. DEV. = 19.1 DEGREES REMARK 500 16 VAL A 6 CG1 - CB - CG2 ANGL. DEV. = -12.0 DEGREES REMARK 500 16 VAL A 6 CA - CB - CG2 ANGL. DEV. = 13.4 DEGREES REMARK 500 17 VAL A 40 CB - CA - C ANGL. DEV. = 12.9 DEGREES REMARK 500 18 VAL A 40 CA - CB - CG1 ANGL. DEV. = 11.1 DEGREES REMARK 500 19 VAL A 6 CG1 - CB - CG2 ANGL. DEV. = -11.7 DEGREES REMARK 500 19 VAL A 6 CA - CB - CG2 ANGL. DEV. = 13.6 DEGREES REMARK 500 20 VAL A 40 CA - CB - CG1 ANGL. DEV. = 13.0 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 HIS A -1 176.26 57.54 REMARK 500 1 ASP A 11 -85.34 -90.36 REMARK 500 1 VAL A 12 -39.78 -138.42 REMARK 500 1 ASP A 32 67.86 -165.08 REMARK 500 1 ASN A 33 5.34 55.22 REMARK 500 1 ASN A 43 65.93 -103.07 REMARK 500 1 GLU A 45 -72.89 67.10 REMARK 500 1 SER A 73 30.77 -73.53 REMARK 500 1 LYS A 75 -11.90 179.11 REMARK 500 2 HIS A -1 178.12 57.24 REMARK 500 2 ASP A 11 -60.13 -108.97 REMARK 500 2 VAL A 12 -68.60 -142.95 REMARK 500 2 SER A 16 -85.26 -81.57 REMARK 500 2 ASN A 17 -39.09 -174.58 REMARK 500 2 ASP A 32 74.04 -155.76 REMARK 500 2 ASN A 33 10.78 58.43 REMARK 500 2 ASN A 55 43.65 -76.73 REMARK 500 2 LYS A 75 -45.58 -154.55 REMARK 500 2 SER A 102 -48.15 -132.11 REMARK 500 3 ASP A 11 -61.92 -106.70 REMARK 500 3 VAL A 12 -46.29 -148.14 REMARK 500 3 ASP A 32 55.46 -158.51 REMARK 500 3 ASN A 33 2.27 51.93 REMARK 500 3 GLU A 45 -74.07 71.14 REMARK 500 3 LYS A 75 -8.08 -151.82 REMARK 500 4 HIS A -1 164.63 178.90 REMARK 500 4 ASP A 11 -63.29 -99.32 REMARK 500 4 VAL A 12 -74.92 -142.93 REMARK 500 4 ASP A 32 48.28 -173.38 REMARK 500 4 ASN A 33 18.67 59.36 REMARK 500 4 ASP A 44 -85.41 -130.54 REMARK 500 4 GLU A 45 -64.09 -131.83 REMARK 500 5 ASP A 11 -63.31 -103.50 REMARK 500 5 VAL A 12 -60.03 -142.68 REMARK 500 5 SER A 16 -86.83 -73.46 REMARK 500 5 ASN A 17 -44.85 175.80 REMARK 500 5 ASP A 32 57.19 -155.64 REMARK 500 5 ASN A 33 -9.92 61.62 REMARK 500 5 VAL A 35 90.66 -65.76 REMARK 500 5 GLU A 45 -69.99 66.33 REMARK 500 5 LYS A 75 13.56 -143.43 REMARK 500 5 SER A 102 -43.21 -140.77 REMARK 500 6 ASN A 3 73.02 47.18 REMARK 500 6 VAL A 12 -55.02 -146.77 REMARK 500 6 ASP A 13 -1.79 -148.80 REMARK 500 6 SER A 16 -85.63 -66.84 REMARK 500 6 ASN A 17 -38.66 -173.53 REMARK 500 6 ILE A 27 96.10 -69.09 REMARK 500 6 ASP A 31 -9.12 -146.00 REMARK 500 6 ASP A 32 65.87 -155.86 REMARK 500 REMARK 500 THIS ENTRY HAS 192 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 GLY A -2 HIS A -1 5 136.86 REMARK 500 ASP A 21 CYS A 22 11 149.31 REMARK 500 GLU A 82 GLY A 83 17 -149.61 REMARK 500 GLY A -2 HIS A -1 18 -146.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 TYR A 79 0.08 SIDE CHAIN REMARK 500 3 TYR A 24 0.08 SIDE CHAIN REMARK 500 8 TYR A 69 0.09 SIDE CHAIN REMARK 500 10 TYR A 24 0.07 SIDE CHAIN REMARK 500 14 TYR A 24 0.07 SIDE CHAIN REMARK 500 14 TYR A 69 0.07 SIDE CHAIN REMARK 500 16 TYR A 79 0.09 SIDE CHAIN REMARK 500 19 TYR A 69 0.08 SIDE CHAIN REMARK 500 20 TYR A 69 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16389 RELATED DB: BMRB REMARK 900 RELATED ID: 376479 RELATED DB: TARGETDB DBREF 2KLA A 1 104 UNP Q57773 Y327_METJA 1 104 SEQADV 2KLA GLY A -2 UNP Q57773 EXPRESSION TAG SEQADV 2KLA HIS A -1 UNP Q57773 EXPRESSION TAG SEQRES 1 A 106 GLY HIS MET ILE ASN MET LYS VAL ALA ILE SER MET ASP SEQRES 2 A 106 VAL ASP LYS ILE SER ASN SER PHE GLU ASP CYS LYS TYR SEQRES 3 A 106 PHE LEU ILE VAL ARG ILE ASP ASP ASN GLU VAL LYS SER SEQRES 4 A 106 THR LYS VAL ILE PHE ASN ASP GLU SER GLY LYS LYS SER SEQRES 5 A 106 ILE VAL LYS GLU ASN VAL ASN ALA ILE ILE CYS LYS ASN SEQRES 6 A 106 ILE SER GLU GLU ASN TYR LYS LYS PHE SER LYS LYS ILE SEQRES 7 A 106 GLU ILE TYR HIS ALA GLU GLY ASP ASP VAL ASP LYS ASN SEQRES 8 A 106 ILE SER LEU PHE ILE GLU GLY GLU LEU SER LYS ILE SER SEQRES 9 A 106 ASN PRO HELIX 1 1 SER A 18 CYS A 22 5 5 HELIX 2 2 GLU A 45 ASN A 55 1 11 HELIX 3 3 SER A 65 SER A 73 1 9 HELIX 4 4 ASP A 85 GLY A 96 1 12 SHEET 1 A 5 VAL A 35 PHE A 42 0 SHEET 2 A 5 TYR A 24 ILE A 30 -1 N PHE A 25 O ILE A 41 SHEET 3 A 5 MET A 4 MET A 10 -1 N MET A 10 O TYR A 24 SHEET 4 A 5 ALA A 58 CYS A 61 1 O ILE A 60 N ALA A 7 SHEET 5 A 5 GLU A 77 HIS A 80 1 O TYR A 79 N ILE A 59 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