HEADER METAL BINDING PROTEIN 07-APR-18 6G81 TITLE SOLUTION STRUCTURE OF THE NI METALLOCHAPERONE HYPA FROM HELICOBACTER TITLE 2 PYLORI COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYDROGENASE MATURATION FACTOR HYPA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI J99; SOURCE 3 ORGANISM_COMMON: CAMPYLOBACTER PYLORI J99; SOURCE 4 ORGANISM_TAXID: 85963; SOURCE 5 STRAIN: J99 / ATCC 700824; SOURCE 6 GENE: HYPA, JHP_0803; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS METALLOCHAPERONE METAL-BINDING NICKEL HYDROGENASE, METAL BINDING KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.A.E.M.SPRONK,S.ZERKO,M.GORKA,W.KOZMINSKI,B.BARDIAUX,B.ZAMBELLI, AUTHOR 2 F.MUSIANI,M.PICCIOLI,H.HU,M.MARONEY,S.CIURLI REVDAT 5 19-JUN-24 6G81 1 REMARK REVDAT 4 14-JUN-23 6G81 1 REMARK REVDAT 3 08-MAY-19 6G81 1 REMARK REVDAT 2 05-DEC-18 6G81 1 JRNL REVDAT 1 10-OCT-18 6G81 0 JRNL AUTH C.A.E.M.SPRONK,S.ZERKO,M.GORKA,W.KOZMINSKI,B.BARDIAUX, JRNL AUTH 2 B.ZAMBELLI,F.MUSIANI,M.PICCIOLI,P.BASAK,F.C.BLUM, JRNL AUTH 3 R.C.JOHNSON,H.HU,D.S.MERRELL,M.MARONEY,S.CIURLI JRNL TITL STRUCTURE AND DYNAMICS OF HELICOBACTER PYLORI JRNL TITL 2 NICKEL-CHAPERONE HYPA: AN INTEGRATED APPROACH USING NMR JRNL TITL 3 SPECTROSCOPY, FUNCTIONAL ASSAYS AND COMPUTATIONAL TOOLS. JRNL REF J. BIOL. INORG. CHEM. V. 23 1309 2018 JRNL REFN ESSN 1432-1327 JRNL PMID 30264175 JRNL DOI 10.1007/S00775-018-1616-Y REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : YASARA REMARK 3 AUTHORS : YASARA BIOSCIENCES REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6G81 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-APR-18. REMARK 100 THE DEPOSITION ID IS D_1200009528. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : 0.2 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-13C; U-15N] HYPA, 20 MM REMARK 210 HEPES, 200 MM SODIUM CHLORIDE, 1 REMARK 210 MM TCEP, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO; 3D REMARK 210 HN(CA)CO; 3D HNCACB; 3D CBCA(CO)NH; 3D HBHANH; 3D HBHA(CO)NH; 3D REMARK 210 HCCH-TOCSY; 2D 1H-13C HSQC AROMATIC; 2D (HB)CB(CGCD)HD; 2D (HB) REMARK 210 CB(CGCDCE)HE; 3D HBCB(CGCD)HD; 3D HBCB(CGCDCE)HE; 3D 1H-13C REMARK 210 NOESY AROMATIC; 4D 13C(ALI)-HMQC-NOESY-13C(ARO)-HSQC; 3D 1H-15N REMARK 210 NOESY; 4D 13C(ALI)-HMQC-NOESY-13C(ALI)-HMQC; 4D 13C-HMQC-NOESY- REMARK 210 15N-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 950 MHZ; 800 MHZ; 600 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DDR2 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; AGILENT REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, SIGNAL SEPARATION REMARK 210 ALGORITHM (SSA), CARA, SPARKY, REMARK 210 TALOS+, YARIA REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 1 ARG A 36 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 ARG A 52 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 HIS A 79 N - CA - C ANGL. DEV. = 18.2 DEGREES REMARK 500 1 ARG A 108 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 ARG A 52 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 ARG A 36 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 ARG A 52 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 4 CYS A 77 N - CA - C ANGL. DEV. = -17.4 DEGREES REMARK 500 6 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 6 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 7 ARG A 36 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 8 ARG A 28 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 8 HIS A 79 N - CA - C ANGL. DEV. = 18.8 DEGREES REMARK 500 9 ASP A 76 CA - C - N ANGL. DEV. = -13.3 DEGREES REMARK 500 9 CYS A 77 N - CA - C ANGL. DEV. = -16.4 DEGREES REMARK 500 9 CYS A 94 N - CA - C ANGL. DEV. = -16.4 DEGREES REMARK 500 10 ARG A 52 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 11 ARG A 52 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 11 ASP A 76 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 11 ASP A 76 CA - C - N ANGL. DEV. = -13.4 DEGREES REMARK 500 11 CYS A 77 N - CA - C ANGL. DEV. = -19.1 DEGREES REMARK 500 11 ARG A 108 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 12 ARG A 28 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 12 ARG A 108 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 12 ARG A 108 NE - CZ - NH2 ANGL. DEV. = 4.5 DEGREES REMARK 500 13 ASP A 76 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 14 ARG A 52 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 14 ARG A 108 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 14 ARG A 108 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 15 ARG A 108 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 17 ARG A 52 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 17 CYS A 77 N - CA - C ANGL. DEV. = -16.5 DEGREES REMARK 500 18 ARG A 28 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 18 CYS A 94 N - CA - C ANGL. DEV. = -16.6 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 ASP A 76 92.57 -36.45 REMARK 500 1 HIS A 79 12.05 -141.20 REMARK 500 1 ASN A 98 65.60 70.64 REMARK 500 2 ASP A 76 94.99 -44.73 REMARK 500 2 HIS A 79 11.84 -140.81 REMARK 500 2 ASP A 87 40.20 -78.12 REMARK 500 2 ASN A 98 63.37 86.45 REMARK 500 2 GLU A 106 -98.08 -145.94 REMARK 500 3 ASP A 76 95.07 -41.69 REMARK 500 3 HIS A 79 13.90 -143.24 REMARK 500 3 ASP A 87 39.82 -79.54 REMARK 500 3 ASN A 98 54.77 104.87 REMARK 500 3 GLU A 106 -128.94 -144.48 REMARK 500 4 ALA A 38 35.16 -83.33 REMARK 500 4 ASP A 76 96.71 -37.18 REMARK 500 4 HIS A 79 11.88 -141.37 REMARK 500 4 LEU A 86 3.70 -65.48 REMARK 500 4 ASN A 98 59.34 76.76 REMARK 500 5 ALA A 38 37.06 -82.66 REMARK 500 5 ASP A 76 94.85 -41.64 REMARK 500 5 ASP A 87 42.85 -82.81 REMARK 500 5 ASN A 98 59.03 90.76 REMARK 500 6 ASP A 76 94.02 -35.05 REMARK 500 6 CYS A 77 78.04 -161.29 REMARK 500 6 HIS A 79 15.81 -142.19 REMARK 500 6 ASP A 87 40.63 -81.97 REMARK 500 6 ASN A 98 64.13 72.21 REMARK 500 7 ALA A 38 30.17 -81.18 REMARK 500 7 ASP A 76 93.96 -39.41 REMARK 500 7 CYS A 77 76.88 -156.59 REMARK 500 7 SER A 78 105.60 -59.09 REMARK 500 7 ASN A 98 56.19 102.20 REMARK 500 7 GLU A 106 -125.10 -137.50 REMARK 500 8 ASP A 76 92.57 -37.54 REMARK 500 8 HIS A 79 11.97 -142.73 REMARK 500 8 LEU A 86 2.00 -64.14 REMARK 500 8 ASP A 87 37.86 -85.47 REMARK 500 8 ASN A 98 57.39 93.85 REMARK 500 8 GLU A 106 -115.91 -143.02 REMARK 500 9 ALA A 38 31.96 -81.55 REMARK 500 9 ASP A 76 91.83 -36.44 REMARK 500 9 HIS A 79 13.71 -142.80 REMARK 500 9 LEU A 86 7.31 -69.62 REMARK 500 9 ASN A 98 57.25 92.96 REMARK 500 10 ASP A 76 93.40 -40.09 REMARK 500 10 CYS A 77 78.58 -161.29 REMARK 500 10 ASP A 87 22.06 -78.89 REMARK 500 10 ASN A 98 42.25 114.10 REMARK 500 11 ASP A 76 98.26 -38.62 REMARK 500 11 HIS A 79 12.27 -140.41 REMARK 500 REMARK 500 THIS ENTRY HAS 93 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 LYS A 75 ASP A 76 1 -149.51 REMARK 500 LYS A 75 ASP A 76 2 -148.43 REMARK 500 LYS A 75 ASP A 76 3 -148.39 REMARK 500 LYS A 75 ASP A 76 5 -148.20 REMARK 500 HIS A 79 VAL A 80 6 -149.68 REMARK 500 LYS A 75 ASP A 76 8 -148.00 REMARK 500 LYS A 75 ASP A 76 12 -145.66 REMARK 500 LYS A 75 ASP A 76 13 -147.13 REMARK 500 LYS A 75 ASP A 76 14 -149.75 REMARK 500 LYS A 75 ASP A 76 16 -149.25 REMARK 500 HIS A 79 VAL A 80 17 -148.52 REMARK 500 LYS A 75 ASP A 76 18 -145.26 REMARK 500 LYS A 75 ASP A 76 20 -149.86 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 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 74 SG REMARK 620 2 CYS A 77 SG 109.3 REMARK 620 3 CYS A 91 SG 110.3 110.0 REMARK 620 4 CYS A 94 SG 110.2 108.3 108.7 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 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34257 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE NI METALLOCHAPERONE HYPA FROM REMARK 900 HELICOBACTER PYLORI DBREF 6G81 A 1 117 UNP P0A0U5 HYPA_HELPJ 1 117 SEQRES 1 A 117 MET HIS GLU TYR SER VAL VAL SER SER LEU ILE ALA LEU SEQRES 2 A 117 CYS GLU GLU HIS ALA LYS LYS ASN GLN ALA HIS LYS ILE SEQRES 3 A 117 GLU ARG VAL VAL VAL GLY ILE GLY GLU ARG SER ALA MET SEQRES 4 A 117 ASP LYS SER LEU PHE VAL SER ALA PHE GLU THR PHE ARG SEQRES 5 A 117 GLU GLU SER LEU VAL CYS LYS ASP ALA ILE LEU ASP ILE SEQRES 6 A 117 VAL ASP GLU LYS VAL GLU LEU GLU CYS LYS ASP CYS SER SEQRES 7 A 117 HIS VAL PHE LYS PRO ASN ALA LEU ASP TYR GLY VAL CYS SEQRES 8 A 117 GLU LYS CYS HIS SER LYS ASN VAL ILE ILE THR GLN GLY SEQRES 9 A 117 ASN GLU MET ARG LEU LEU SER LEU GLU MET LEU ALA GLU HET ZN A 201 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 AA1 HIS A 2 ASN A 21 1 20 HELIX 2 AA2 ASP A 40 GLU A 53 1 14 SHEET 1 AA1 3 ILE A 62 GLU A 68 0 SHEET 2 AA1 3 ALA A 23 GLY A 34 1 N VAL A 29 O ILE A 62 SHEET 3 AA1 3 ARG A 108 ALA A 116 -1 O LEU A 115 N LYS A 25 SHEET 1 AA2 2 GLU A 71 CYS A 74 0 SHEET 2 AA2 2 VAL A 99 GLN A 103 -1 O ILE A 100 N GLU A 73 LINK SG CYS A 74 ZN ZN A 201 1555 1555 2.34 LINK SG CYS A 77 ZN ZN A 201 1555 1555 2.35 LINK SG CYS A 91 ZN ZN A 201 1555 1555 2.34 LINK SG CYS A 94 ZN ZN A 201 1555 1555 2.37 SITE 1 AC1 4 CYS A 74 CYS A 77 CYS A 91 CYS A 94 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