HEADER ISOMERASE 07-DEC-09 2KR7 TITLE SOLUTION STRUCTURE OF HELICOBACTER PYLORI SLYD COMPND MOL_ID: 1; COMPND 2 MOLECULE: FKBP-TYPE PEPTIDYL-PROLYL CIS-TRANS ISOMERASE SLYD; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-151; COMPND 5 SYNONYM: PPIASE, ROTAMASE; COMPND 6 EC: 5.2.1.8; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_COMMON: CAMPYLOBACTER PYLORI; SOURCE 4 ORGANISM_TAXID: 210; SOURCE 5 STRAIN: 26695; SOURCE 6 GENE: SLYD, HP_1123; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET-32A(+) KEYWDS PROTEIN, ISOMERASE, ROTAMASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.CHENG,H.LI,W.XIA,K.SZE,H.SUN REVDAT 2 01-MAY-24 2KR7 1 REMARK REVDAT 1 15-DEC-10 2KR7 0 JRNL AUTH T.CHENG,H.LI,W.XIA,K.SZE,H.SUN JRNL TITL SOLUTION STRUCTURE OF HELICOBACTER PYLORI SLYD JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA,_AMBER, CYANA,_AMBER, CYANA,_AMBER REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA,_AMBER), REMARK 3 GUNTERT, MUMENTHALER AND WUTHRICH (CYANA,_AMBER), REMARK 3 CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLM (CYANA,_AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KR7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1000101472. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1-1.5 MM [U-100% 13C; U-100% REMARK 210 15N] SLYD-1, 90% H2O/10% D2O; 1- REMARK 210 1.5 MM [U-100% 13C; U-100% 15N] REMARK 210 SLYD-2, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCACB; 3D REMARK 210 HNCO; 3D HN(CA)CO; 3D C(CO)NH; REMARK 210 3D H(CCO)NH; 3D HCCH-TOCSY; 3D REMARK 210 HCCH-COSY; 3D HBHA(CO)NH; 3D REMARK 210 HNHA; 3D HN(CO)CA; 3D 1H-15N REMARK 210 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,_AMBER REMARK 210 METHOD USED : MOLECULAR DYNAMICS, SIMULATED REMARK 210 ANNEALING 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 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 9 ARG A 20 NE - CZ - NH1 ANGL. DEV. = 3.0 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 LYS A 34 -72.97 -78.09 REMARK 500 1 ILE A 41 109.75 -47.86 REMARK 500 1 ASP A 106 20.41 -75.08 REMARK 500 1 ALA A 131 -176.33 -67.76 REMARK 500 1 GLU A 149 55.48 -90.94 REMARK 500 1 GLU A 150 -73.19 -138.19 REMARK 500 2 SER A 8 8.27 -69.36 REMARK 500 2 LYS A 34 -73.32 -107.87 REMARK 500 2 ILE A 41 104.58 -56.69 REMARK 500 2 ASP A 87 -36.43 -133.30 REMARK 500 2 LEU A 130 77.07 -111.31 REMARK 500 3 HIS A 4 -83.96 -74.26 REMARK 500 3 LYS A 34 -74.02 -79.48 REMARK 500 3 THR A 43 -37.79 -131.05 REMARK 500 3 GLU A 71 -56.66 -147.04 REMARK 500 3 TYR A 73 70.85 42.51 REMARK 500 3 SER A 79 52.51 -145.14 REMARK 500 3 ARG A 86 10.76 -69.73 REMARK 500 3 LYS A 96 90.48 -66.99 REMARK 500 3 ASP A 106 13.21 -69.30 REMARK 500 3 LEU A 130 76.78 -104.40 REMARK 500 4 LYS A 34 -73.58 -107.47 REMARK 500 4 ILE A 41 106.09 -50.70 REMARK 500 4 ASP A 87 -50.52 -130.63 REMARK 500 4 GLU A 149 -71.75 -84.49 REMARK 500 5 LYS A 34 -72.47 -78.59 REMARK 500 5 ILE A 41 106.74 -46.37 REMARK 500 5 ALA A 72 -70.57 -72.33 REMARK 500 5 SER A 79 79.26 -108.41 REMARK 500 5 GLU A 90 66.97 21.28 REMARK 500 5 LYS A 96 21.94 -71.81 REMARK 500 5 HIS A 128 83.77 48.46 REMARK 500 6 ILE A 41 107.69 -50.73 REMARK 500 6 ALA A 72 -67.53 -132.35 REMARK 500 6 ASP A 87 -50.36 -132.38 REMARK 500 7 GLU A 7 20.84 -75.97 REMARK 500 7 GLN A 22 93.45 -67.60 REMARK 500 7 LYS A 34 -72.17 -92.01 REMARK 500 7 ILE A 41 109.30 -47.57 REMARK 500 7 ALA A 72 -67.45 -125.51 REMARK 500 7 TYR A 80 8.03 56.55 REMARK 500 7 ALA A 131 96.49 -67.50 REMARK 500 8 GLU A 7 52.72 -102.08 REMARK 500 8 SER A 8 2.46 -69.70 REMARK 500 8 LYS A 34 -75.80 -104.27 REMARK 500 8 THR A 43 -49.61 -134.27 REMARK 500 8 ASP A 87 -50.14 -132.42 REMARK 500 9 LYS A 34 -87.97 -117.59 REMARK 500 9 ILE A 41 109.22 -54.85 REMARK 500 9 LYS A 52 0.24 -68.03 REMARK 500 REMARK 500 THIS ENTRY HAS 117 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 2KR7 A 1 151 UNP O25748 SLYD_HELPY 1 151 SEQRES 1 A 151 MET GLN ASN HIS ASP LEU GLU SER ILE LYS GLN ALA ALA SEQRES 2 A 151 LEU ILE GLU TYR GLU VAL ARG GLU GLN GLY SER SER ILE SEQRES 3 A 151 VAL LEU ASP SER ASN ILE SER LYS GLU PRO LEU GLU PHE SEQRES 4 A 151 ILE ILE GLY THR ASN GLN ILE ILE ALA GLY LEU GLU LYS SEQRES 5 A 151 ALA VAL LEU LYS ALA GLN ILE GLY GLU TRP GLU GLU VAL SEQRES 6 A 151 VAL ILE ALA PRO GLU GLU ALA TYR GLY VAL TYR GLU SER SEQRES 7 A 151 SER TYR LEU GLN GLU VAL PRO ARG ASP GLN PHE GLU GLY SEQRES 8 A 151 ILE GLU LEU GLU LYS GLY MET SER VAL PHE GLY GLN THR SEQRES 9 A 151 GLU ASP ASN GLN THR ILE GLN ALA ILE ILE LYS ASP PHE SEQRES 10 A 151 SER ALA THR HIS VAL MET VAL ASP TYR ASN HIS PRO LEU SEQRES 11 A 151 ALA GLY LYS THR LEU ALA PHE ARG PHE LYS VAL LEU GLY SEQRES 12 A 151 PHE ARG GLU VAL SER GLU GLU GLU HELIX 1 1 ILE A 47 LEU A 55 1 9 HELIX 2 2 ASP A 87 GLU A 90 5 4 SHEET 1 A 3 VAL A 27 SER A 30 0 SHEET 2 A 3 ALA A 12 GLU A 21 -1 N VAL A 19 O ASP A 29 SHEET 3 A 3 LEU A 37 ILE A 40 -1 O PHE A 39 N ALA A 13 SHEET 1 B 4 VAL A 27 SER A 30 0 SHEET 2 B 4 ALA A 12 GLU A 21 -1 N VAL A 19 O ASP A 29 SHEET 3 B 4 LEU A 135 ARG A 145 -1 O ARG A 138 N GLU A 18 SHEET 4 B 4 TRP A 62 ILE A 67 -1 N GLU A 63 O PHE A 139 SHEET 1 C 4 TYR A 80 PRO A 85 0 SHEET 2 C 4 HIS A 121 TYR A 126 -1 O VAL A 122 N VAL A 84 SHEET 3 C 4 GLN A 108 PHE A 117 -1 N ASP A 116 O MET A 123 SHEET 4 C 4 SER A 99 THR A 104 -1 N VAL A 100 O ALA A 112 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