HEADER DE NOVO PROTEIN 29-JUN-11 2LFD TITLE SOLUTION NMR STRUCTURE OF DIIRON PROTEIN IN PRESENCE OF 2 EQ ZN2+, TITLE 2 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET OR21 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIIRON PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_VECTOR: BL21 KEYWDS FOUR-HELIX BUNDLE, STRUCTURAL GENOMICS, PSI-BIOLOGY, PROTEIN KEYWDS 2 STRUCTURE INITIATIVE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, KEYWDS 3 NESG, DE NOVO PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.WU,M.PIRES,J.L.MILLS,A.REIG,T.SZYPERSKI,W.DEGRADO,G.T.MONTELIONE, AUTHOR 2 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 3 07-MAR-12 2LFD 1 AUTHOR JRNL REVDAT 2 22-FEB-12 2LFD 1 KEYWDS REVDAT 1 24-AUG-11 2LFD 0 JRNL AUTH Y.WU,M.PIRES,J.L.MILLS,A.REIG,T.SZYPERSKI,G.T.MONTELIONE, JRNL AUTH 2 W.DEGRADO JRNL TITL SOLUTION NMR STRUCTURE OF DIIRON PROTEIN IN PRESENCE OF 2 EQ JRNL TITL 2 ZN2+ JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LFD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUL-11. REMARK 100 THE RCSB ID CODE IS RCSB102323. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.8 REMARK 210 IONIC STRENGTH : 0.2 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-100% 13C; U-100% 15N] REMARK 210 PROTEIN, 95% H2O/5% D2O; 0.3 MM REMARK 210 [U-10% 13C; U-100% 15N] PROTEIN, REMARK 210 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCO; 3D REMARK 210 HNCACB; 3D HBHA(CO)NH; 3D CCH- REMARK 210 TOCSY; 3D HN(CA)CO; (4,3)D HCCH; REMARK 210 15N,13C-SIMNOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AUTOSTRUCTURE, CYANA, NMRPIPE, REMARK 210 XEASY, PSVS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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: 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 OE1 GLU A 53 HZ2 LYS A 57 1.60 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 GLU A 3 121.99 71.43 REMARK 500 1 LYS A 86 -60.68 -93.39 REMARK 500 2 ASP A 2 94.80 66.19 REMARK 500 2 LEU A 4 -31.73 -132.32 REMARK 500 2 SER A 85 -179.23 72.97 REMARK 500 3 ASP A 29 -83.53 -87.33 REMARK 500 3 GLU A 30 -58.95 -173.04 REMARK 500 3 GLN A 87 -162.37 61.92 REMARK 500 4 SER A 85 -80.09 72.78 REMARK 500 4 LYS A 86 -62.28 -149.31 REMARK 500 4 LYS A 113 46.54 -91.47 REMARK 500 5 ALA A 58 108.77 -52.81 REMARK 500 5 ALA A 90 -57.46 71.89 REMARK 500 5 LYS A 113 34.90 -83.75 REMARK 500 6 LYS A 86 97.53 -175.63 REMARK 500 6 GLN A 87 120.23 69.84 REMARK 500 7 LEU A 4 -47.76 68.57 REMARK 500 7 LYS A 86 -51.73 73.90 REMARK 500 7 LYS A 113 -145.03 -76.54 REMARK 500 7 LYS A 114 -50.15 -146.71 REMARK 500 8 LYS A 113 -103.68 -87.67 REMARK 500 8 LYS A 114 -55.92 -147.93 REMARK 500 9 GLU A 3 49.50 -76.22 REMARK 500 9 LEU A 4 -63.86 -151.82 REMARK 500 9 ARG A 59 -70.53 70.61 REMARK 500 9 GLN A 87 93.67 54.73 REMARK 500 10 GLU A 27 -82.82 -71.43 REMARK 500 10 ASP A 29 149.64 68.68 REMARK 500 10 GLU A 30 -76.56 58.00 REMARK 500 11 LYS A 86 -44.57 -133.32 REMARK 500 11 LYS A 114 110.81 170.84 REMARK 500 12 LEU A 4 -36.52 -130.01 REMARK 500 12 SER A 85 97.26 -63.48 REMARK 500 12 LYS A 114 -160.04 179.52 REMARK 500 13 GLN A 87 101.95 72.40 REMARK 500 14 GLU A 3 30.51 -88.54 REMARK 500 14 GLN A 87 -47.04 -139.98 REMARK 500 14 LYS A 114 -106.24 61.37 REMARK 500 15 LEU A 4 -30.73 -173.66 REMARK 500 15 LYS A 86 -54.49 -137.89 REMARK 500 17 ASP A 2 -84.37 -60.07 REMARK 500 17 LYS A 114 -1.46 77.95 REMARK 500 18 GLU A 3 83.78 64.07 REMARK 500 18 SER A 85 -81.65 67.09 REMARK 500 18 LYS A 86 14.85 -153.79 REMARK 500 18 LYS A 113 103.12 47.02 REMARK 500 19 LEU A 4 -73.81 -112.30 REMARK 500 19 LYS A 86 -52.33 -139.93 REMARK 500 19 ALA A 90 -89.59 48.62 REMARK 500 20 GLU A 3 -77.12 74.31 REMARK 500 REMARK 500 THIS ENTRY HAS 51 RAMACHANDRAN OUTLIERS. 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 1 ZN A 300 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 74 OE1 REMARK 620 2 GLU A 44 OE2 98.9 REMARK 620 3 HIS A 77 ND1 92.9 162.8 REMARK 620 4 HIS A 100 NE2 169.4 91.7 76.8 REMARK 620 5 GLU A 44 OE1 100.5 67.4 98.2 83.4 REMARK 620 6 GLU A 104 OE1 73.8 93.8 101.6 105.8 159.6 REMARK 620 7 GLU A 104 OE2 97.8 94.9 95.9 81.3 156.2 24.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 ZN A 400 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 107 ND1 REMARK 620 2 GLU A 11 OE1 103.6 REMARK 620 3 GLU A 74 OE2 100.0 126.6 REMARK 620 4 GLU A 104 OE1 104.0 112.5 107.0 REMARK 620 5 GLU A 11 OE2 146.0 50.9 84.4 106.8 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 400 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17749 RELATED DB: BMRB REMARK 900 RELATED ID: OR21 RELATED DB: TARGETDB DBREF 2LFD A 1 115 PDB 2LFD 2LFD 1 115 SEQRES 1 A 115 MET ASP GLU LEU ARG GLU LEU LEU LYS ALA GLU GLN GLN SEQRES 2 A 115 GLY ILE LYS ILE LEU LYS GLU VAL LEU LYS LYS ALA LYS SEQRES 3 A 115 GLU GLY ASP GLU GLN GLU LEU ALA ARG LEU ASN GLN GLU SEQRES 4 A 115 ILE VAL LYS ALA GLU LYS GLN GLY VAL LYS VAL TYR LYS SEQRES 5 A 115 GLU ALA ALA GLU LYS ALA ARG ASN PRO GLU LYS ARG GLN SEQRES 6 A 115 VAL ILE ASP LYS ILE LEU GLU ASP GLU GLU LYS HIS ILE SEQRES 7 A 115 GLU TRP HIS LYS ALA ALA SER LYS GLN GLY ASN ALA GLU SEQRES 8 A 115 GLN PHE ALA SER LEU VAL GLN GLN HIS LEU GLN ASP GLU SEQRES 9 A 115 GLN ARG HIS VAL GLU GLU ILE GLU LYS LYS ASN HET ZN A 300 1 HET ZN A 400 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 LEU A 4 GLY A 28 1 25 HELIX 2 2 ASP A 29 LYS A 57 1 29 HELIX 3 3 ASN A 60 SER A 85 1 26 HELIX 4 4 ASN A 89 LYS A 113 1 25 LINK OE1 GLU A 74 ZN ZN A 300 1555 1555 1.71 LINK ND1 HIS A 107 ZN ZN A 400 1555 1555 1.96 LINK OE2 GLU A 44 ZN ZN A 300 1555 1555 2.17 LINK ND1 HIS A 77 ZN ZN A 300 1555 1555 2.19 LINK NE2 HIS A 100 ZN ZN A 300 1555 1555 2.43 LINK OE1 GLU A 11 ZN ZN A 400 1555 1555 1.57 LINK OE2 GLU A 74 ZN ZN A 400 1555 1555 1.59 LINK OE1 GLU A 44 ZN ZN A 300 1555 1555 1.59 LINK OE1 GLU A 104 ZN ZN A 400 1555 1555 1.60 LINK OE1 GLU A 104 ZN ZN A 300 1555 1555 3.55 LINK OE2 GLU A 104 ZN ZN A 300 1555 1555 1.62 LINK OE2 GLU A 11 ZN ZN A 400 1555 1555 2.79 SITE 1 AC1 5 GLU A 44 GLU A 74 HIS A 77 HIS A 100 SITE 2 AC1 5 GLU A 104 SITE 1 AC2 4 GLU A 11 GLU A 74 GLU A 104 HIS A 107 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