10 20 30 40 50 60 70 80 1XJS - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 24-SEP-04 1XJS
TITLE SOLUTION STRUCTURE OF IRON-SULFUR CLUSTER ASSEMBLY PROTEIN TITLE 2 ISCU FROM BACILLUS SUBTILIS, WITH ZINC BOUND AT THE ACTIVE TITLE 3 SITE. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET SR17
COMPND MOL_ID: 1; COMPND 2 MOLECULE: NIFU-LIKE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: IRON-SULFUR CLUSTER ASSEMBLY PROTEIN ISCU; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 GENE: NIFU; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PMGK; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21D
KEYWDS SR17, NMR STRUCTURE, AUTOSTRUCTURE, IRON-SULFUR, ZINC, KEYWDS 2 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG, NIFU-LIKE, KEYWDS 3 PROTEIN STRUCTURE INITIATIVE, STRUCTURAL GENOMICS, PSI, KEYWDS 4 UNKNOWN FUNCTION
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR G.J.KORNHABER,G.V.T.SWAPNA,T.A.RAMELOT,J.R.CORT,M.A.KENNEDY, AUTHOR 2 G.T.MONTELIONE,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM AUTHOR 3 (NESG)
REVDAT 3 24-FEB-09 1XJS 1 VERSN REVDAT 2 08-MAR-05 1XJS 1 AUTHOR REVDAT 1 04-JAN-05 1XJS 0
JRNL AUTH G.J.KORNHABER,G.V.T.SWAPNA,T.A.RAMELOT,J.R.CORT, JRNL AUTH 2 M.A.KENNEDY,G.T.MONTELIONE JRNL TITL SOLUTION STRUCTURE OF IRON-SULFUR CLUSTER ASSEMBLY JRNL TITL 2 PROTEIN ISCU FROM BACILLUS SUBTILIS, WITH ZINC JRNL TITL 3 BOUND AT THE ACTIVE SITE. NORTHEAST STRUCTURAL JRNL TITL 4 GENOMICS CONSORTIUM TARGET SR17. JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 2.0.6, CNS 1.0 REMARK 3 AUTHORS : SCHWIETERS, ET AL. (X-PLOR), BRUNGER, ET AL. REMARK 3 (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1XJS COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-OCT-04. REMARK 100 THE RCSB ID CODE IS RCSB030434.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 100MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 100MM POTASSIUM PHOSPHATE, REMARK 210 200MM GLYCEROL, 1MM DTT, 0.02% REMARK 210 NAN3, 5% D2O, 95% H2O; 20MM REMARK 210 SODIUM PHOSPHATE, 50MM SODIUM REMARK 210 CHLORIDE, 10MM DTT, 0.02% REMARK 210 NAN3, 95% H2O, 5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D-TOCSYS, 13C,1H-HSQC, 15N, REMARK 210 1H-HSQC, 15N,1H-HSQC, 2D REMARK 210 HOMONUCLEAR NOESY, 4D_13C- REMARK 210 SEPARATED_NOESY, 3D_13C- REMARK 210 SEPARATED_NOESY, 3D_15N- REMARK 210 SEPARATED_NOESY, H/D EXCHANGE REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ, 800 MHZ, 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AUTOASSIGN 1.9, AUTOSTRUCTURE REMARK 210 2.0.0, TALOS 2.1, HYPER & REMARK 210 PDBSTAT 3.2 AND 3.32, NMRPIPE REMARK 210 2.1, SPARKY 3.106 REMARK 210 METHOD USED : MINIMAL CONSTRAINT STRUCTURE REMARK 210 CONTAINED 492 CONFORMATIONALLY REMARK 210 RESTRICTING NOE-DERIVED REMARK 210 DISTANCE CONSTRAINTS, 108 REMARK 210 HYDROGEN BOND CONSTRAINTS, AND REMARK 210 197 DIHEDRAL ANGLE REMARK 210 CONSTRAINTS. THIS RESULTED IN REMARK 210 5.9 CONSTRAINTS PER RESIDUE REMARK 210 AND 1.2 LONG RANGE CONSTRAINTS REMARK 210 PER RESIDUE. STRUCTURE REMARK 210 DETERMINATION WAS PERFORMED REMARK 210 WITH THE FOLLOWING STEPS: REMARK 210 AUTOSTRUCTURE-DYANA WAS USED REMARK 210 TO IDENTIFY DISTANCE REMARK 210 CONSTRAINTS. THESE DISTANCE REMARK 210 CONSTRAINTS WERE USED AS INPUT REMARK 210 INTO A SIMULATED ANNEALING REMARK 210 WITH XPLOR-NIH. THE TOP TEN REMARK 210 STRUCTURES WERE ENERGY REMARK 210 MINIMIZED WITH WATER USING CNS. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 60 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING A SELECTIVE REMARK 210 ISOTOPIC LABELING STRATEGY INVOLVING THE PROTONATION OF REMARK 210 SPECIFIC RESIDUES IN A PERDEUTERATED BACKGROUND. PROTONATED REMARK 210 ATOMS INCLUDE: ILE HD1, VAL HG*, LEU HD*. ALL TYR AND PHE SIDE REMARK 210 -CHAINS ARE PROTONATED. IN ADDITION TO THE ATOMS MENTIONED REMARK 210 ABOVE, EXCHANGEABLE ATOMS WERE PROTONATED.
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 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 LYS A 25 94.33 72.64 REMARK 500 1 ASP A 30 -72.88 -152.98 REMARK 500 1 SER A 31 -71.89 -113.88 REMARK 500 1 ASP A 52 72.54 -109.72 REMARK 500 1 ASP A 54 20.48 -142.66 REMARK 500 1 ILE A 55 -162.60 -127.37 REMARK 500 1 LYS A 83 -168.60 -127.55 REMARK 500 1 ASP A 84 -165.98 -120.15 REMARK 500 1 LYS A 102 -80.95 169.94 REMARK 500 1 GLU A 103 109.50 -166.20 REMARK 500 1 TYR A 104 142.05 -173.67 REMARK 500 1 ALA A 141 -175.84 68.86 REMARK 500 1 GLU A 143 -104.89 60.15 REMARK 500 2 ASN A 6 93.82 -49.93 REMARK 500 2 LEU A 7 -15.49 76.61 REMARK 500 2 ARG A 23 25.97 -162.99 REMARK 500 2 ASN A 24 36.93 -95.83 REMARK 500 2 ASP A 30 -73.35 -141.94 REMARK 500 2 SER A 31 -85.32 -95.26 REMARK 500 2 ASP A 52 67.14 -105.93 REMARK 500 2 LYS A 83 -155.53 -134.12 REMARK 500 2 LYS A 102 -89.00 -163.26 REMARK 500 2 GLU A 103 84.18 177.71 REMARK 500 2 ASP A 106 -78.43 58.10 REMARK 500 2 ALA A 141 178.21 74.43 REMARK 500 2 GLU A 143 -67.64 65.89 REMARK 500 2 GLU A 144 -44.13 -164.56 REMARK 500 3 ASN A 6 -79.70 -148.01 REMARK 500 3 LEU A 7 -43.39 -141.43 REMARK 500 3 LEU A 28 79.22 -115.80 REMARK 500 3 SER A 31 -104.31 -144.56 REMARK 500 3 PRO A 39 -79.88 -16.81 REMARK 500 3 ASP A 43 -71.03 -20.86 REMARK 500 3 ASP A 52 66.33 -114.25 REMARK 500 3 ILE A 55 -164.00 -110.21 REMARK 500 3 GLU A 57 -71.37 -81.70 REMARK 500 3 TYR A 104 141.89 -173.43 REMARK 500 3 LEU A 131 -70.92 -52.95 REMARK 500 3 ALA A 141 155.82 68.15 REMARK 500 3 GLU A 143 117.87 66.73 REMARK 500 3 GLU A 144 -88.30 -78.07 REMARK 500 4 SER A 2 40.11 -150.25 REMARK 500 4 ASN A 6 -76.65 -59.14 REMARK 500 4 ASN A 21 71.23 -117.95 REMARK 500 4 PRO A 22 38.50 -75.85 REMARK 500 4 ASP A 30 -90.85 -141.73 REMARK 500 4 SER A 31 -65.59 -108.39 REMARK 500 4 PRO A 39 40.31 -65.58 REMARK 500 4 THR A 40 -36.69 -178.10 REMARK 500 4 ASP A 54 30.13 -143.15 REMARK 500 4 ASP A 109 96.73 -68.34 REMARK 500 4 LEU A 110 -55.31 -148.48 REMARK 500 4 LYS A 121 5.04 -157.37 REMARK 500 4 ALA A 141 162.25 72.96 REMARK 500 4 GLU A 143 -161.27 65.39 REMARK 500 5 PHE A 3 -34.53 -149.04 REMARK 500 5 ASN A 6 -114.69 -158.57 REMARK 500 5 LEU A 7 -18.32 72.67 REMARK 500 5 ARG A 23 -159.67 59.33 REMARK 500 5 ASP A 30 -73.45 -143.71 REMARK 500 5 SER A 31 -62.37 -124.67 REMARK 500 5 THR A 40 -22.68 78.93 REMARK 500 5 ASP A 43 -67.26 -29.71 REMARK 500 5 ASP A 54 30.71 -142.31 REMARK 500 5 ASP A 84 -162.53 -120.39 REMARK 500 5 LYS A 102 -82.65 -177.89 REMARK 500 5 GLU A 103 97.49 -176.36 REMARK 500 5 ASP A 106 -82.11 52.73 REMARK 500 5 ILE A 108 33.62 70.80 REMARK 500 5 VAL A 140 17.35 -144.77 REMARK 500 5 LYS A 142 30.01 -159.93 REMARK 500 5 GLU A 143 -85.67 64.55 REMARK 500 5 GLU A 144 -25.88 177.93 REMARK 500 6 PHE A 3 -66.48 72.89 REMARK 500 6 ALA A 5 145.90 66.05 REMARK 500 6 LYS A 25 106.71 -164.52 REMARK 500 6 ASP A 30 -57.76 -164.34 REMARK 500 6 SER A 31 -77.04 -115.63 REMARK 500 6 PRO A 39 122.74 -34.27 REMARK 500 6 THR A 40 -7.57 77.32 REMARK 500 6 CYS A 41 -46.67 -130.86 REMARK 500 6 ASP A 52 66.33 -115.16 REMARK 500 6 LYS A 102 89.71 59.04 REMARK 500 6 GLU A 103 -28.11 -162.87 REMARK 500 6 LYS A 142 -56.19 176.76 REMARK 500 6 GLU A 143 -166.25 157.09 REMARK 500 7 PHE A 3 -79.63 -164.19 REMARK 500 7 ASN A 4 137.95 -175.06 REMARK 500 7 LYS A 25 19.91 -163.13 REMARK 500 7 ASP A 30 -87.10 -115.61 REMARK 500 7 SER A 31 -80.71 -92.68 REMARK 500 7 PRO A 39 -64.30 -25.15 REMARK 500 7 ASP A 52 68.61 -115.11 REMARK 500 7 ILE A 55 -166.42 -125.84 REMARK 500 7 LYS A 83 -156.91 -133.66 REMARK 500 7 LYS A 102 -37.32 73.11 REMARK 500 7 TYR A 104 -154.32 -120.19 REMARK 500 7 ASP A 106 -4.70 86.04 REMARK 500 7 LEU A 110 -55.44 -147.74 REMARK 500 7 SER A 120 -17.34 -46.44 REMARK 500 7 LYS A 121 26.63 -164.04 REMARK 500 7 ALA A 141 172.46 69.64 REMARK 500 7 GLU A 143 -164.58 -66.35 REMARK 500 7 GLU A 144 77.74 -108.30 REMARK 500 8 SER A 2 -84.74 -135.49 REMARK 500 8 ARG A 23 -74.46 -57.71 REMARK 500 8 ASN A 24 114.46 -177.53 REMARK 500 8 ASP A 30 -71.31 -150.21 REMARK 500 8 SER A 31 -70.70 -117.00 REMARK 500 8 PRO A 39 48.78 -65.69 REMARK 500 8 THR A 40 -45.94 -159.72 REMARK 500 8 ASP A 54 33.64 -150.43 REMARK 500 8 ASP A 84 -162.37 -116.30 REMARK 500 8 GLN A 100 -40.41 -140.78 REMARK 500 8 TYR A 104 -148.24 -95.54 REMARK 500 8 ALA A 141 94.28 69.58 REMARK 500 8 GLU A 143 -75.42 70.11 REMARK 500 8 GLU A 144 95.58 -177.97 REMARK 500 9 SER A 2 -38.73 -131.98 REMARK 500 9 PHE A 3 36.06 -88.23 REMARK 500 9 ARG A 23 -142.53 -79.96 REMARK 500 9 ASP A 30 -75.64 -127.62 REMARK 500 9 PRO A 39 41.42 -70.46 REMARK 500 9 THR A 40 -10.18 158.22 REMARK 500 9 ASP A 54 21.25 -145.38 REMARK 500 9 ASP A 84 -168.96 -116.03 REMARK 500 9 LYS A 102 -69.03 73.23 REMARK 500 9 ASP A 106 96.19 -49.76 REMARK 500 9 ILE A 108 -15.83 75.28 REMARK 500 9 LEU A 110 36.04 -89.81 REMARK 500 9 LYS A 121 27.65 -169.34 REMARK 500 9 ALA A 141 152.27 169.59 REMARK 500 9 GLU A 143 -76.13 67.50 REMARK 500 9 GLU A 144 95.21 -172.38 REMARK 500 10 ARG A 23 17.20 -145.44 REMARK 500 10 LYS A 25 24.81 -165.64 REMARK 500 10 ASP A 30 -69.70 -127.58 REMARK 500 10 SER A 31 -51.13 -127.04 REMARK 500 10 PRO A 39 -64.93 -21.56 REMARK 500 10 ASP A 52 65.77 -100.06 REMARK 500 10 ASP A 54 28.80 -142.63 REMARK 500 10 GLU A 57 -69.98 -91.48 REMARK 500 10 GLN A 100 -42.49 -134.40 REMARK 500 10 TYR A 104 -145.99 -117.02 REMARK 500 10 ASP A 106 -4.34 70.35 REMARK 500 10 ILE A 108 -36.94 71.32 REMARK 500 10 LEU A 110 74.21 -150.84 REMARK 500 10 SER A 120 -16.25 -43.52 REMARK 500 10 LYS A 142 54.20 179.68 REMARK 500 10 GLU A 143 -99.18 60.51 REMARK 500 10 GLU A 144 -66.53 -171.15 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 150 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 43 OD1 REMARK 620 2 CYS A 41 SG 95.3 REMARK 620 3 ASP A 43 OD2 76.6 167.4 REMARK 620 4 CYS A 66 SG 158.9 104.3 85.3 REMARK 620 5 CYS A 128 SG 83.7 86.5 102.0 89.6 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 150
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: SR17 RELATED DB: TARGETDB
DBREF 1XJS A 1 147 UNP O32163 NIFU_BACSU 1 147
SEQRES 1 A 147 MET SER PHE ASN ALA ASN LEU ASP THR LEU TYR ARG GLN SEQRES 2 A 147 VAL ILE MET ASP HIS TYR LYS ASN PRO ARG ASN LYS GLY SEQRES 3 A 147 VAL LEU ASN ASP SER ILE VAL VAL ASP MET ASN ASN PRO SEQRES 4 A 147 THR CYS GLY ASP ARG ILE ARG LEU THR MET LYS LEU ASP SEQRES 5 A 147 GLY ASP ILE VAL GLU ASP ALA LYS PHE GLU GLY GLU GLY SEQRES 6 A 147 CYS SER ILE SER MET ALA SER ALA SER MET MET THR GLN SEQRES 7 A 147 ALA ILE LYS GLY LYS ASP ILE GLU THR ALA LEU SER MET SEQRES 8 A 147 SER LYS ILE PHE SER ASP MET MET GLN GLY LYS GLU TYR SEQRES 9 A 147 ASP ASP SER ILE ASP LEU GLY ASP ILE GLU ALA LEU GLN SEQRES 10 A 147 GLY VAL SER LYS PHE PRO ALA ARG ILE LYS CYS ALA THR SEQRES 11 A 147 LEU SER TRP LYS ALA LEU GLU LYS GLY VAL ALA LYS GLU SEQRES 12 A 147 GLU GLY GLY ASN
HET ZN A 150 1
HETNAM ZN ZINC ION
FORMUL 2 ZN ZN 2+
HELIX 1 1 LEU A 7 ASN A 21 1 15 HELIX 2 2 CYS A 66 LYS A 81 1 16 HELIX 3 3 ASP A 84 LYS A 102 1 19 HELIX 4 4 LEU A 110 SER A 120 1 11 HELIX 5 5 ARG A 125 VAL A 140 1 16
SHEET 1 A 3 ILE A 32 ASN A 37 0 SHEET 2 A 3 ARG A 44 LYS A 50 -1 O LEU A 47 N VAL A 34 SHEET 3 A 3 ASP A 58 GLU A 64 -1 O GLU A 64 N ARG A 44
LINK ZN ZN A 150 OD1 ASP A 43 1555 1555 1.66 LINK ZN ZN A 150 SG CYS A 41 1555 1555 2.47 LINK ZN ZN A 150 OD2 ASP A 43 1555 1555 1.75 LINK ZN ZN A 150 SG CYS A 66 1555 1555 2.43 LINK ZN ZN A 150 SG CYS A 128 1555 1555 2.59
SITE 1 AC1 4 CYS A 41 ASP A 43 CYS A 66 CYS A 128
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