PDB Short entry for 3O7T HEADER ISOMERASE 31-JUL-10 3O7T TITLE CRYSTAL STRUCTURE OF CYCLOPHILIN A FROM MONILIOPHTHORA PERNICIOSA COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLOPHILIN A; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MONILIOPHTHORA PERNICIOSA; SOURCE 3 ORGANISM_TAXID: 153609; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS CYCLOPHILIN, PEPTIDYL-PROLYL CIS-TRANS ISOMERASE, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR P.S.MONZANI,H.M.PEREIRA,K.P.GRAMACHO,F.V.MEIRELLES,G.OLIVA, AUTHOR 2 J.C.M.CASCARDO REVDAT 2 21-FEB-24 3O7T 1 REMARK REVDAT 1 10-AUG-11 3O7T 0 JRNL AUTH P.S.MONZANI,H.M.PEREIRA,K.P.GRAMACHO,F.V.MEIRELLES,G.OLIVA, JRNL AUTH 2 J.C.M.CASCARDO JRNL TITL CRYSTAL STRUCTURES OF APO-CYCLOPHILIN AND BOUNDED JRNL TITL 2 CYCLOSPORINE A FROM MONILIOPHTHORA PERNICIOSA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6_289 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 17081 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 868 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 36.8818 - 3.3612 0.98 2984 162 0.1718 0.2018 REMARK 3 2 3.3612 - 2.6681 0.97 2831 132 0.1495 0.1864 REMARK 3 3 2.6681 - 2.3309 0.95 2713 163 0.1458 0.2067 REMARK 3 4 2.3309 - 2.1178 0.93 2655 141 0.1527 0.1818 REMARK 3 5 2.1178 - 1.9660 0.90 2566 133 0.1747 0.2405 REMARK 3 6 1.9660 - 1.8501 0.87 2464 137 0.2154 0.2491 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.37 REMARK 3 B_SOL : 80.00 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.100 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.68520 REMARK 3 B22 (A**2) : 6.43750 REMARK 3 B33 (A**2) : -2.74960 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.011 1301 REMARK 3 ANGLE : 1.254 1754 REMARK 3 CHIRALITY : 0.088 189 REMARK 3 PLANARITY : 0.005 229 REMARK 3 DIHEDRAL : 15.217 468 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3O7T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000060773. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUN-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 10.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LNLS REMARK 200 BEAMLINE : W01B-MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.43 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.2.25 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18133 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 73.749 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.14500 REMARK 200 R SYM (I) : 0.14500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.56800 REMARK 200 R SYM FOR SHELL (I) : 0.56800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 400, 100MM CAPS PH 10.5., REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 18.92700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.10300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 55.84100 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 18.92700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.10300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 55.84100 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 18.92700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.10300 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 55.84100 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 18.92700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.10300 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 55.84100 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 168 LIES ON A SPECIAL POSITION. 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 12 1.36 81.36 REMARK 500 ALA A 26 -51.60 -122.69 REMARK 500 PHE A 58 -73.99 -147.74 REMARK 500 ASN A 69 6.73 -153.45 REMARK 500 REMARK 500 REMARK: NULL DBREF 3O7T A -1 162 PDB 3O7T 3O7T -1 162 SEQRES 1 A 164 SER HIS MET ALA ASN VAL PHE PHE ASN ILE SER ILE ASN SEQRES 2 A 164 ASP LYS PRO GLU GLY ARG ILE VAL PHE LYS LEU TYR ASP SEQRES 3 A 164 GLU ALA VAL PRO LYS THR ALA LYS ASN PHE ARG GLU LEU SEQRES 4 A 164 ALA THR GLY GLN HIS GLY PHE GLY TYR LYS ASP SER ILE SEQRES 5 A 164 PHE HIS ARG VAL ILE PRO GLN PHE MET LEU GLN GLY GLY SEQRES 6 A 164 ASP PHE THR ARG HIS ASN GLY THR GLY GLY LYS SER ILE SEQRES 7 A 164 TYR GLY GLU LYS PHE ALA ASP GLU ASN PHE GLN VAL LYS SEQRES 8 A 164 HIS THR LYS PRO GLY LEU LEU SER MET ALA ASN ALA GLY SEQRES 9 A 164 ALA ASN THR ASN GLY SER GLN PHE PHE ILE THR THR VAL SEQRES 10 A 164 PRO THR SER TRP LEU ASP GLY LYS HIS VAL VAL PHE GLY SEQRES 11 A 164 GLU VAL ILE GLU GLY LEU ASP ILE VAL ARG LYS VAL GLU SEQRES 12 A 164 GLY LYS GLY SER ALA SER GLY LYS THR ASN ALA THR ILE SEQRES 13 A 164 LYS ILE THR ASP CYS GLY THR VAL FORMUL 2 HOH *178(H2 O) HELIX 1 1 VAL A 27 GLY A 40 1 14 HELIX 2 2 THR A 117 ASP A 121 5 5 HELIX 3 3 GLY A 133 GLY A 142 1 10 SHEET 1 A 8 ARG A 53 ILE A 55 0 SHEET 2 A 8 MET A 59 GLY A 62 -1 O GLN A 61 N ARG A 53 SHEET 3 A 8 PHE A 110 THR A 113 -1 O PHE A 110 N GLY A 62 SHEET 4 A 8 LEU A 95 MET A 98 -1 N SER A 97 O PHE A 111 SHEET 5 A 8 VAL A 126 GLU A 132 -1 O PHE A 127 N LEU A 96 SHEET 6 A 8 LYS A 13 LEU A 22 -1 N VAL A 19 O ILE A 131 SHEET 7 A 8 VAL A 4 ILE A 10 -1 N VAL A 4 O PHE A 20 SHEET 8 A 8 ILE A 154 THR A 161 -1 O ASP A 158 N ASN A 7 CRYST1 37.854 98.206 111.682 90.00 90.00 90.00 I 2 2 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 0.026417 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010183 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008954 0.00000