PDB Short entry for 1A33 HEADER ISOMERASE 27-JAN-98 1A33 TITLE PEPTIDYLPROLYL ISOMERASE, CYCLOPHILIN-LIKE DOMAIN FROM BRUGIA MALAYI COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYLPROLYL ISOMERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CYCLOPHILIN-LIKE DOMAIN; COMPND 5 EC: 5.2.1.8; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BRUGIA MALAYI; SOURCE 3 ORGANISM_TAXID: 6279; SOURCE 4 ATCC: ATCC 75593; SOURCE 5 COLLECTION: ATCC 75593; SOURCE 6 GENE: BMCYP-1; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: ER2267; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: DOUBLE STRAND VECTOR (TAC, PMB1 AND SOURCE 11 AMPR); SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PMAL-C2; SOURCE 13 EXPRESSION_SYSTEM_GENE: MBP FUSION PROTEIN KEYWDS ISOMERASE, PEPTIDYL-PROLYL CIS-TRANS, PEPTIDYLPROLYL ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR V.MIKOL,D.MA,C.K.S.CARLOW REVDAT 3 02-AUG-23 1A33 1 REMARK REVDAT 2 24-FEB-09 1A33 1 VERSN REVDAT 1 29-JUL-98 1A33 0 JRNL AUTH V.MIKOL,D.MA,C.K.CARLOW JRNL TITL CRYSTAL STRUCTURE OF THE CYCLOPHILIN-LIKE DOMAIN FROM THE JRNL TITL 2 PARASITIC NEMATODE BRUGIA MALAYI. JRNL REF PROTEIN SCI. V. 7 1310 1998 JRNL REFN ISSN 0961-8368 JRNL PMID 9655334 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 13236 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 677 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.25 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1520 REMARK 3 BIN R VALUE (WORKING SET) : 0.2010 REMARK 3 BIN FREE R VALUE : 0.1700 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 76 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1338 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 234 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.75 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.450 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARHCSX.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1A33 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170331. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JUL-96 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : ENRAF-NONIUS FR591 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MACSCIENCE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13361 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : 0.05000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 36.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.08000 REMARK 200 R SYM FOR SHELL (I) : 0.08000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 22.00 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.851 REMARK 200 STARTING MODEL: PDB ENTRY 1CWA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE INITIAL 6 UL DROP CONSISTED OF 50 REMARK 280 MM MES-NAOH PH 6.0, 0.9 M (NH4)2SO4, 1MM PROTEIN. THE 1 ML REMARK 280 RESERVOIR SOLUTION CONSISTED OF 100 MM MES-NAOH PH 6.0, 1.8 M REMARK 280 (NH4)2SO4 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.06500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.95000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.95000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 35.03250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.95000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.95000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 105.09750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.95000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.95000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 35.03250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.95000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.95000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 105.09750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 70.06500 REMARK 290 REMARK 290 REMARK: NULL 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 LYS A 3 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 4 CG CD CE NZ 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 ASP A 5 43.39 -108.02 REMARK 500 PHE A 71 -55.74 -139.58 REMARK 500 ILE A 136 -45.72 -130.97 REMARK 500 LEU A 176 -158.09 -120.03 REMARK 500 REMARK 500 REMARK: NULL DBREF 1A33 A 1 177 UNP Q27450 CYP1_BRUMA 1 177 SEQRES 1 A 177 MET SER LYS LYS ASP ARG ARG ARG VAL PHE LEU ASP VAL SEQRES 2 A 177 THR ILE ASP GLY ASN LEU ALA GLY ARG ILE VAL MET GLU SEQRES 3 A 177 LEU TYR ASN ASP ILE ALA PRO ARG THR CYS ASN ASN PHE SEQRES 4 A 177 LEU MET LEU CYS THR GLY MET ALA GLY THR GLY LYS ILE SEQRES 5 A 177 SER GLY LYS PRO LEU HIS TYR LYS GLY SER THR PHE HIS SEQRES 6 A 177 ARG VAL ILE LYS ASN PHE MET ILE GLN GLY GLY ASP PHE SEQRES 7 A 177 THR LYS GLY ASP GLY THR GLY GLY GLU SER ILE TYR GLY SEQRES 8 A 177 GLY MET PHE ASP ASP GLU GLU PHE VAL MET LYS HIS ASP SEQRES 9 A 177 GLU PRO PHE VAL VAL SER MET ALA ASN LYS GLY PRO ASN SEQRES 10 A 177 THR ASN GLY SER GLN PHE PHE ILE THR THR THR PRO ALA SEQRES 11 A 177 PRO HIS LEU ASN ASN ILE HIS VAL VAL PHE GLY LYS VAL SEQRES 12 A 177 VAL SER GLY GLN GLU VAL VAL THR LYS ILE GLU TYR LEU SEQRES 13 A 177 LYS THR ASN SER LYS ASN ARG PRO LEU ALA ASP VAL VAL SEQRES 14 A 177 ILE LEU ASN CYS GLY GLU LEU VAL FORMUL 2 HOH *234(H2 O) HELIX 1 1 PRO A 33 THR A 44 1 12 HELIX 2 2 PRO A 131 LEU A 133 5 3 HELIX 3 3 GLN A 147 GLU A 154 1 8 SHEET 1 A 8 VAL A 168 GLU A 175 0 SHEET 2 A 8 ARG A 7 ILE A 15 -1 N THR A 14 O VAL A 169 SHEET 3 A 8 ASN A 18 LEU A 27 -1 N LEU A 27 O ARG A 7 SHEET 4 A 8 VAL A 139 SER A 145 -1 N SER A 145 O VAL A 24 SHEET 5 A 8 VAL A 108 MET A 111 -1 N VAL A 109 O PHE A 140 SHEET 6 A 8 PHE A 123 THR A 126 -1 N PHE A 124 O SER A 110 SHEET 7 A 8 MET A 72 GLY A 75 -1 N GLY A 75 O PHE A 123 SHEET 8 A 8 PHE A 64 ILE A 68 -1 N ILE A 68 O MET A 72 CRYST1 57.900 57.900 140.130 90.00 90.00 90.00 P 41 21 2 8 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 0.017271 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017271 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007136 0.00000