HEADER ISOMERASE 20-FEB-98 1A58 TITLE CYCLOPHILIN FROM BRUGIA MALAYI COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLOPHILIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CYCLOPHILIN DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BRUGIA MALAYI; SOURCE 3 ORGANISM_TAXID: 6279; SOURCE 4 GENE: CYCLOPHILIN; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: XL-1 BLUE SUPERCOMPETANT; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PMAL-C2; SOURCE 9 EXPRESSION_SYSTEM_GENE: CYCLOPHILIN KEYWDS ISOMERASE, PPIASE EXPDTA X-RAY DIFFRACTION AUTHOR P.TAYLOR,A.P.PAGE,G.KONTOPIDIS,H.HUSI,M.D.WALKINSHAW REVDAT 3 07-FEB-24 1A58 1 REMARK REVDAT 2 24-FEB-09 1A58 1 VERSN REVDAT 1 27-MAY-98 1A58 0 JRNL AUTH P.TAYLOR,A.P.PAGE,G.KONTOPIDIS,H.HUSI,M.D.WALKINSHAW JRNL TITL THE X-RAY STRUCTURE OF A DIVERGENT CYCLOPHILIN FROM THE JRNL TITL 2 NEMATODE PARASITE BRUGIA MALAYI. JRNL REF FEBS LETT. V. 425 361 1998 JRNL REFN ISSN 0014-5793 JRNL PMID 9559680 JRNL DOI 10.1016/S0014-5793(98)00264-6 REMARK 2 REMARK 2 RESOLUTION. 1.95 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 17458 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 881 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.04 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1936 REMARK 3 BIN R VALUE (WORKING SET) : 0.2880 REMARK 3 BIN FREE R VALUE : 0.3090 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 97 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1365 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 154 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.85 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.20 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) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.426 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.01 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.358 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.900 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 5.100 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.800 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.600 ; 2.500 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM19.SOL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SHELX97 WAS USED INITIALLY WITH SAME REMARK 3 CROSS-VALIDATION DATA REMARK 4 REMARK 4 1A58 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_1000170407. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR 3.851 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM IMIDAZOLE AT PH6.5, 15% SAT. REMARK 280 AMMONIUM SULFATE 0.02% SODIUM AZIDE, 0.56 MM PROTEIN CONC. 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 70.97200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 29.10750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 29.10750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 35.48600 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 29.10750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 29.10750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 106.45800 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 29.10750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.10750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 35.48600 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 29.10750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.10750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 106.45800 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 70.97200 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 H1 HOH A 202 H2 HOH A 244 1.23 REMARK 500 H2 HOH A 179 H1 HOH A 235 1.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 H2 HOH A 254 H2 HOH A 254 7555 1.11 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 HIS A 58 135.84 -171.29 REMARK 500 PHE A 71 -58.07 -133.34 REMARK 500 REMARK 500 REMARK: NULL DBREF 1A58 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 *154(H2 O) HELIX 1 1 LYS A 3 ASP A 5 5 3 HELIX 2 2 PRO A 33 THR A 44 1 12 HELIX 3 3 PRO A 131 LEU A 133 5 3 HELIX 4 4 GLN A 147 GLU A 154 1 8 SHEET 1 A 8 VAL A 168 LEU A 176 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 58.215 58.215 141.944 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 0.017178 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017178 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007045 0.00000