10 20 30 40 50 60 70 80 2KDX - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER METAL-BINDING PROTEIN 20-JAN-09 2KDX
TITLE SOLUTION STRUCTURE OF HYPA PROTEIN
COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYDROGENASE/UREASE NICKEL INCORPORATION PROTEIN COMPND 3 HYPA; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: HYPA; COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_COMMON: CAMPYLOBACTER PYLORI; SOURCE 4 ORGANISM_TAXID: 85962; SOURCE 5 STRAIN: 26695; SOURCE 6 GENE: HP_0869, HYPA; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 11 EXPRESSION_SYSTEM_VECTOR: PGBHIS
KEYWDS METALLOCHAPERONE, HYDROGENASE, METAL-BINDING, NICKEL, METAL- KEYWDS 2 BINDING PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR W.XIA,H.LI,K.-H.SZE
REVDAT 1 20-OCT-09 2KDX 0
JRNL AUTH W.XIA,H.LI,K.-H.SZE,H.SUN JRNL TITL STRUCTURE OF A NICKEL CHAPERONE, HYPA, FROM JRNL TITL 2 HELICOBACTER PYLORI REVEALS TWO DISTINCT METAL JRNL TITL 3 BINDING SITES JRNL REF J.AM.CHEM.SOC. V. 131 10031 2009 JRNL REFN ISSN 0002-7863 JRNL PMID 19621959 JRNL DOI 10.1021/JA900543Y
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 7.0 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2KDX COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-JAN-09. REMARK 100 THE RCSB ID CODE IS RCSB101000.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM [U-99% 13C; U-99% 15N] REMARK 210 HYPA-1, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C REMARK 210 HSQC; 3D HNCO; 3D HN(CA)CO; 3D REMARK 210 CBCA(CO)NH; 3D HNCACB; 3D HCCH REMARK 210 -COSY; 3D HCCH-TOCSY; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.1 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: 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 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 1 ARG A 110 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 10 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 11 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 16 ARG A 110 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 17 ARG A 110 NE - CZ - NH1 ANGL. DEV. = 3.1 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 1 MET A 3 40.99 -78.72 REMARK 500 1 HIS A 26 22.64 49.89 REMARK 500 1 GLU A 29 -51.48 -125.14 REMARK 500 1 ALA A 40 9.96 57.37 REMARK 500 1 LYS A 77 -70.44 -55.48 REMARK 500 1 CYS A 79 -146.32 -115.55 REMARK 500 1 SER A 80 42.34 -158.25 REMARK 500 1 ASN A 86 -68.03 -136.21 REMARK 500 1 LEU A 88 -63.38 -133.29 REMARK 500 2 HIS A 26 9.84 55.68 REMARK 500 2 ALA A 40 13.55 58.68 REMARK 500 2 CYS A 79 -154.33 -141.74 REMARK 500 2 SER A 80 16.85 -149.96 REMARK 500 2 ASN A 86 -57.45 -145.56 REMARK 500 2 LEU A 88 -69.49 -129.42 REMARK 500 2 HIS A 97 64.76 -61.48 REMARK 500 3 HIS A 26 2.10 54.20 REMARK 500 3 GLU A 29 -53.23 -122.73 REMARK 500 3 CYS A 79 -157.95 -142.52 REMARK 500 3 SER A 80 37.69 -149.65 REMARK 500 3 ASN A 86 -76.51 -144.25 REMARK 500 3 LEU A 88 -67.77 -131.66 REMARK 500 3 HIS A 97 57.67 -65.25 REMARK 500 3 LEU A 117 90.77 -67.09 REMARK 500 4 SER A 2 93.05 -69.11 REMARK 500 4 HIS A 26 4.15 56.33 REMARK 500 4 GLU A 29 -60.40 -93.24 REMARK 500 4 CYS A 79 -155.24 -142.69 REMARK 500 4 SER A 80 18.48 -147.90 REMARK 500 4 ALA A 87 -179.50 56.30 REMARK 500 4 LEU A 88 -51.15 -134.78 REMARK 500 5 HIS A 26 4.65 54.25 REMARK 500 5 ALA A 40 3.05 58.29 REMARK 500 5 ASP A 42 93.56 -69.50 REMARK 500 5 CYS A 79 -159.78 -146.24 REMARK 500 5 SER A 80 63.08 -150.52 REMARK 500 5 ASN A 86 -58.23 -142.09 REMARK 500 5 LEU A 88 -63.02 -131.42 REMARK 500 6 MET A 3 94.87 -67.03 REMARK 500 6 HIS A 4 -36.71 -135.05 REMARK 500 6 HIS A 26 5.93 56.73 REMARK 500 6 ALA A 40 16.86 56.03 REMARK 500 6 LYS A 77 -70.23 -64.82 REMARK 500 6 ASP A 78 59.86 -115.07 REMARK 500 6 CYS A 79 -153.27 -143.89 REMARK 500 6 SER A 80 14.24 -147.42 REMARK 500 6 ALA A 87 176.97 56.50 REMARK 500 6 LEU A 88 -51.06 -134.04 REMARK 500 6 LYS A 95 -75.41 -79.28 REMARK 500 7 HIS A 26 18.06 55.01 REMARK 500 7 ALA A 40 9.97 55.27 REMARK 500 7 CYS A 79 -156.83 -141.62 REMARK 500 7 SER A 80 33.33 -151.02 REMARK 500 7 ASN A 86 -58.48 -136.03 REMARK 500 7 LEU A 88 -67.60 -131.19 REMARK 500 7 ALA A 118 -59.14 -135.60 REMARK 500 8 HIS A 26 16.31 52.75 REMARK 500 8 ALA A 40 19.74 56.54 REMARK 500 8 CYS A 79 -156.06 -141.02 REMARK 500 8 ASN A 86 -60.30 -130.52 REMARK 500 8 LEU A 88 -67.66 -131.74 REMARK 500 8 ALA A 118 -10.27 61.70 REMARK 500 9 HIS A 26 13.61 52.70 REMARK 500 9 ALA A 40 0.77 56.89 REMARK 500 9 LYS A 77 -72.76 -62.25 REMARK 500 9 ASP A 78 55.44 -113.69 REMARK 500 9 CYS A 79 -155.13 -138.31 REMARK 500 9 SER A 80 26.58 -148.57 REMARK 500 9 ASN A 86 -68.18 -138.49 REMARK 500 9 LEU A 88 -68.56 -132.96 REMARK 500 9 LYS A 95 -62.78 -93.72 REMARK 500 10 MET A 3 12.69 57.97 REMARK 500 10 HIS A 26 2.25 56.23 REMARK 500 10 ALA A 40 16.70 55.85 REMARK 500 10 CYS A 79 -155.59 -142.17 REMARK 500 10 SER A 80 25.70 -146.78 REMARK 500 10 ASN A 86 -65.47 -143.67 REMARK 500 10 LEU A 88 -69.29 -129.36 REMARK 500 10 ASN A 100 1.10 -67.83 REMARK 500 10 ALA A 118 -68.77 -140.79 REMARK 500 11 SER A 2 93.83 -66.22 REMARK 500 11 HIS A 4 -69.67 -129.28 REMARK 500 11 HIS A 26 3.52 53.57 REMARK 500 11 ALA A 40 -1.54 57.31 REMARK 500 11 CYS A 79 -157.91 -143.86 REMARK 500 11 SER A 80 33.35 -147.48 REMARK 500 11 ASN A 86 -61.49 -141.44 REMARK 500 11 LEU A 88 -40.02 -131.59 REMARK 500 11 TYR A 90 -87.63 -103.44 REMARK 500 11 ALA A 118 -58.21 -153.47 REMARK 500 12 HIS A 4 -61.16 -129.90 REMARK 500 12 HIS A 26 26.82 48.42 REMARK 500 12 GLU A 29 -65.32 -94.26 REMARK 500 12 ALA A 40 10.36 56.06 REMARK 500 12 CYS A 79 -155.40 -140.88 REMARK 500 12 SER A 80 61.65 -152.49 REMARK 500 12 ASN A 86 81.83 58.02 REMARK 500 12 LEU A 112 -50.58 -126.28 REMARK 500 12 LEU A 117 101.60 -56.93 REMARK 500 13 HIS A 26 6.39 54.93 REMARK 500 13 GLU A 29 -60.43 -95.36 REMARK 500 13 ALA A 40 7.05 55.87 REMARK 500 13 CYS A 79 -150.77 -136.21 REMARK 500 13 SER A 80 17.75 -146.10 REMARK 500 13 ASN A 86 -63.30 -134.72 REMARK 500 13 LYS A 99 30.19 -90.89 REMARK 500 13 ALA A 118 -50.08 -148.52 REMARK 500 14 HIS A 26 11.64 54.25 REMARK 500 14 ALA A 40 13.32 56.90 REMARK 500 14 CYS A 79 -156.50 -142.25 REMARK 500 14 SER A 80 12.80 -145.77 REMARK 500 15 GLU A 29 -56.68 -120.05 REMARK 500 15 ALA A 40 18.68 57.59 REMARK 500 15 LYS A 77 -75.86 -61.14 REMARK 500 15 CYS A 79 -153.12 -140.27 REMARK 500 15 ASN A 86 -68.97 -143.15 REMARK 500 15 HIS A 97 67.34 -59.71 REMARK 500 15 LEU A 112 -57.80 -125.86 REMARK 500 15 ALA A 118 -13.36 -143.11 REMARK 500 16 HIS A 26 12.87 53.43 REMARK 500 16 ALA A 40 -6.12 58.71 REMARK 500 16 CYS A 79 -156.75 -143.94 REMARK 500 16 SER A 80 15.37 -145.08 REMARK 500 16 LEU A 112 -60.15 -109.34 REMARK 500 17 HIS A 26 26.67 48.53 REMARK 500 17 GLU A 29 -62.47 -99.84 REMARK 500 17 ALA A 40 10.64 57.09 REMARK 500 17 CYS A 79 -156.07 -142.30 REMARK 500 17 SER A 80 30.41 -148.50 REMARK 500 17 ASN A 86 -68.48 -139.27 REMARK 500 17 LEU A 88 -66.08 -128.79 REMARK 500 18 MET A 3 26.44 -71.12 REMARK 500 18 HIS A 26 19.12 51.31 REMARK 500 18 ALA A 40 3.53 57.71 REMARK 500 18 CYS A 79 -159.98 -147.05 REMARK 500 18 SER A 80 23.41 -146.04 REMARK 500 18 ASN A 86 -13.71 92.31 REMARK 500 19 HIS A 26 10.99 54.71 REMARK 500 19 GLU A 29 -62.47 -105.24 REMARK 500 19 ALA A 40 0.28 59.78 REMARK 500 19 CYS A 79 -159.23 -145.22 REMARK 500 19 SER A 80 18.22 -144.32 REMARK 500 19 ASN A 86 -5.54 81.17 REMARK 500 19 HIS A 97 58.89 -64.09 REMARK 500 19 ALA A 118 -18.11 59.72 REMARK 500 20 HIS A 4 -2.27 -143.14 REMARK 500 20 HIS A 26 10.33 55.84 REMARK 500 20 GLU A 29 -63.08 -108.40 REMARK 500 20 ALA A 40 16.08 56.55 REMARK 500 20 CYS A 79 -157.56 -144.04 REMARK 500 20 ASN A 86 -10.40 77.59 REMARK 500 20 HIS A 97 59.17 -64.57 REMARK 500 20 LEU A 112 -60.49 -124.30 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 120 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 76 SG REMARK 620 2 CYS A 79 SG 108.6 REMARK 620 3 CYS A 93 SG 109.5 109.3 REMARK 620 4 CYS A 96 SG 109.7 109.6 110.1 REMARK 620 N 1 2 3
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 120
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16126 RELATED DB: BMRB
DBREF 2KDX A 3 119 UNP P0A0U4 HYPA_HELPY 1 117
SEQADV 2KDX GLY A 1 UNP P0A0U4 EXPRESSION TAG SEQADV 2KDX SER A 2 UNP P0A0U4 EXPRESSION TAG
SEQRES 1 A 119 GLY SER MET HIS GLU TYR SER VAL VAL SER SER LEU ILE SEQRES 2 A 119 ALA LEU CYS GLU GLU HIS ALA LYS LYS ASN GLN ALA HIS SEQRES 3 A 119 LYS ILE GLU ARG VAL VAL VAL GLY ILE GLY GLU ARG SER SEQRES 4 A 119 ALA MET ASP LYS SER LEU PHE VAL SER ALA PHE GLU THR SEQRES 5 A 119 PHE ARG GLU GLU SER LEU VAL CYS LYS ASP ALA ILE LEU SEQRES 6 A 119 ASP ILE VAL ASP GLU LYS VAL GLU LEU GLU CYS LYS ASP SEQRES 7 A 119 CYS SER HIS VAL PHE LYS PRO ASN ALA LEU ASP TYR GLY SEQRES 8 A 119 VAL CYS GLU LYS CYS HIS SER LYS ASN VAL ILE ILE THR SEQRES 9 A 119 GLN GLY ASN GLU MET ARG LEU LEU SER LEU GLU MET LEU SEQRES 10 A 119 ALA GLU
HET ZN A 120 1
HETNAM ZN ZINC ION
FORMUL 2 ZN ZN 2+
HELIX 1 1 MET A 3 ASN A 23 1 21 HELIX 2 2 ASP A 42 ARG A 54 1 13 HELIX 3 3 GLU A 55 SER A 57 5 3
SHEET 1 A 3 LEU A 65 GLU A 70 0 SHEET 2 A 3 ARG A 30 GLY A 36 1 N VAL A 33 O VAL A 68 SHEET 3 A 3 ARG A 110 GLU A 115 -1 O ARG A 110 N GLY A 34 SHEET 1 B 3 VAL A 82 PHE A 83 0 SHEET 2 B 3 GLU A 73 GLU A 75 -1 N LEU A 74 O PHE A 83 SHEET 3 B 3 ILE A 102 GLN A 105 -1 O GLN A 105 N GLU A 73
LINK SG CYS A 76 ZN ZN A 120 1555 1555 2.23 LINK SG CYS A 79 ZN ZN A 120 1555 1555 2.24 LINK SG CYS A 93 ZN ZN A 120 1555 1555 2.23 LINK SG CYS A 96 ZN ZN A 120 1555 1555 2.22
SITE 1 AC1 4 CYS A 76 CYS A 79 CYS A 93 CYS A 96
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