PDB Short entry for 2KGJ HEADER ISOMERASE 12-MAR-09 2KGJ TITLE SOLUTION STRUCTURE OF PARVULIN DOMAIN OF PPID FROM E.COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE D; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 264-357; COMPND 5 SYNONYM: PPIASE D, ROTAMASE D; COMPND 6 EC: 5.2.1.8; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: PPID, YBAU, B0441, JW0431; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET 11A KEYWDS PROLYL ISOMERASE, PARVULIN, CELL INNER MEMBRANE, CELL MEMBRANE, KEYWDS 2 ISOMERASE, MEMBRANE, ROTAMASE, STRESS RESPONSE, TRANSMEMBRANE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR U.WEININGER,R.P.JAKOB REVDAT 3 01-MAY-24 2KGJ 1 REMARK REVDAT 2 26-FEB-20 2KGJ 1 REMARK SEQADV REVDAT 1 19-JAN-10 2KGJ 0 JRNL AUTH U.WEININGER,R.P.JAKOB,M.KOVERMANN,J.BALBACH,F.X.SCHMID JRNL TITL THE PROLYL ISOMERASE DOMAIN OF PPID FROM ESCHERICHIA COLI JRNL TITL 2 SHOWS A PARVULIN FOLD BUT IS DEVOID OF CATALYTIC ACTIVITY. JRNL REF PROTEIN SCI. V. 19 6 2009 JRNL REFN ISSN 0961-8368 JRNL PMID 19866485 JRNL DOI 10.1002/PRO.277 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 2.0, ARIA 2.0 REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES (ARIA), LINGE, REMARK 3 O'DONOGHUE AND NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KGJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000101092. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 100 MM POTASSIUM PHOSPHATE-1, 5 REMARK 210 MM [U-15N] PROTEIN, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 3D 1H-15N TOCSY; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ARIA 2.0 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 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: 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 OE2 GLU A 18 HZ1 LYS A 39 1.57 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 SER A 76 53.24 77.99 REMARK 500 1 ALA A 96 -66.55 72.01 REMARK 500 1 HIS A 98 95.30 -68.72 REMARK 500 1 HIS A 99 -64.99 -179.76 REMARK 500 1 HIS A 100 -59.65 -149.02 REMARK 500 1 HIS A 101 114.23 -162.99 REMARK 500 2 SER A 76 60.37 78.64 REMARK 500 2 ALA A 96 -84.33 63.76 REMARK 500 2 HIS A 98 49.90 -98.05 REMARK 500 2 HIS A 99 87.73 53.93 REMARK 500 2 HIS A 100 -27.23 75.05 REMARK 500 3 SER A 76 46.20 78.56 REMARK 500 3 ALA A 96 -75.89 -112.21 REMARK 500 3 HIS A 98 -78.03 -128.75 REMARK 500 3 HIS A 99 -39.15 -146.27 REMARK 500 3 HIS A 101 93.06 -69.38 REMARK 500 4 SER A 76 45.79 78.10 REMARK 500 4 ALA A 95 -37.38 73.27 REMARK 500 4 ALA A 96 102.17 -52.80 REMARK 500 4 HIS A 97 -6.54 70.79 REMARK 500 5 SER A 76 56.12 78.49 REMARK 500 5 ALA A 95 34.41 -90.31 REMARK 500 5 ALA A 96 -61.39 71.32 REMARK 500 5 HIS A 99 -74.05 -116.42 REMARK 500 5 HIS A 100 -72.52 -118.01 REMARK 500 6 LYS A 70 -60.10 -102.66 REMARK 500 6 SER A 76 45.71 78.15 REMARK 500 6 HIS A 97 115.40 75.35 REMARK 500 6 HIS A 98 -44.81 -145.73 REMARK 500 6 HIS A 99 -72.54 -176.29 REMARK 500 7 SER A 76 57.82 76.33 REMARK 500 7 ALA A 95 45.42 -85.02 REMARK 500 7 ALA A 96 -162.27 63.23 REMARK 500 7 HIS A 97 -99.71 -94.31 REMARK 500 7 HIS A 98 -72.70 62.35 REMARK 500 7 HIS A 99 -14.53 -153.96 REMARK 500 8 SER A 76 59.98 78.87 REMARK 500 8 HIS A 97 -44.36 74.87 REMARK 500 9 SER A 76 60.95 78.98 REMARK 500 9 ALA A 96 85.06 56.08 REMARK 500 9 HIS A 97 -142.98 69.21 REMARK 500 9 HIS A 98 -47.17 74.49 REMARK 500 9 HIS A 101 24.28 -161.12 REMARK 500 10 SER A 76 49.71 79.25 REMARK 500 10 ALA A 95 -53.29 72.83 REMARK 500 10 HIS A 101 75.85 54.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16211 RELATED DB: BMRB DBREF 2KGJ A 1 94 UNP P0ADY1 PPID_ECOLI 264 357 SEQADV 2KGJ ALA A 95 UNP P0ADY1 EXPRESSION TAG SEQADV 2KGJ ALA A 96 UNP P0ADY1 EXPRESSION TAG SEQADV 2KGJ HIS A 97 UNP P0ADY1 EXPRESSION TAG SEQADV 2KGJ HIS A 98 UNP P0ADY1 EXPRESSION TAG SEQADV 2KGJ HIS A 99 UNP P0ADY1 EXPRESSION TAG SEQADV 2KGJ HIS A 100 UNP P0ADY1 EXPRESSION TAG SEQADV 2KGJ HIS A 101 UNP P0ADY1 EXPRESSION TAG SEQADV 2KGJ HIS A 102 UNP P0ADY1 EXPRESSION TAG SEQRES 1 A 102 THR GLN PRO GLN ARG THR ARG TYR SER ILE ILE GLN THR SEQRES 2 A 102 LYS THR GLU ASP GLU ALA LYS ALA VAL LEU ASP GLU LEU SEQRES 3 A 102 ASN LYS GLY GLY ASP PHE ALA ALA LEU ALA LYS GLU LYS SEQRES 4 A 102 SER ALA ASP ILE ILE SER ALA ARG ASN GLY GLY ASP MET SEQRES 5 A 102 GLY TRP LEU GLU ASP ALA THR ILE PRO ASP GLU LEU LYS SEQRES 6 A 102 ASN ALA GLY LEU LYS GLU LYS GLY GLN LEU SER GLY VAL SEQRES 7 A 102 ILE LYS SER SER VAL GLY PHE LEU ILE VAL ARG LEU ASP SEQRES 8 A 102 ASP ILE GLN ALA ALA HIS HIS HIS HIS HIS HIS HELIX 1 1 THR A 15 GLY A 29 1 15 HELIX 2 2 ASP A 31 LYS A 39 1 9 HELIX 3 3 ASP A 42 ARG A 47 1 6 HELIX 4 4 PRO A 61 ASN A 66 1 6 SHEET 1 A 4 ASP A 51 GLU A 56 0 SHEET 2 A 4 ARG A 5 THR A 13 -1 N THR A 6 O LEU A 55 SHEET 3 A 4 GLY A 84 GLN A 94 -1 O PHE A 85 N THR A 13 SHEET 4 A 4 LEU A 75 SER A 81 -1 N ILE A 79 O LEU A 86 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