HEADER ISOMERASE 24-SEP-09 3K0M TITLE CRYOGENIC STRUCTURE OF CYPA COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLOPHILIN A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A, PPIASE A, ROTAMASE A, COMPND 5 CYCLOSPORIN A-BINDING PROTEIN; COMPND 6 EC: 5.2.1.8; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PPIA, CYPA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROLINE ISOMERASE, CYCLOSPORIN, HOST-VIRUS INTERACTION, ISOMERASE, KEYWDS 2 ISOPEPTIDE BOND, PHOSPHOPROTEIN, ROTAMASE EXPDTA X-RAY DIFFRACTION AUTHOR J.S.FRASER,T.ALBER REVDAT 3 06-SEP-23 3K0M 1 REMARK REVDAT 2 19-JUN-13 3K0M 1 JRNL VERSN REVDAT 1 08-DEC-09 3K0M 0 JRNL AUTH J.S.FRASER,M.W.CLARKSON,S.C.DEGNAN,R.ERION,D.KERN,T.ALBER JRNL TITL HIDDEN ALTERNATIVE STRUCTURES OF PROLINE ISOMERASE ESSENTIAL JRNL TITL 2 FOR CATALYSIS. JRNL REF NATURE V. 462 669 2009 JRNL REFN ISSN 0028-0836 JRNL PMID 19956261 JRNL DOI 10.1038/NATURE08615 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.4_162) 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) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.120 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 52646 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.131 REMARK 3 R VALUE (WORKING SET) : 0.129 REMARK 3 FREE R VALUE : 0.149 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 2637 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 33.6717 - 3.3345 0.99 2918 168 0.1558 0.1637 REMARK 3 2 3.3345 - 2.6470 0.99 2778 158 0.1399 0.1282 REMARK 3 3 2.6470 - 2.3125 0.99 2769 148 0.1341 0.1550 REMARK 3 4 2.3125 - 2.1011 0.99 2744 140 0.1181 0.1264 REMARK 3 5 2.1011 - 1.9505 0.99 2755 130 0.1142 0.1564 REMARK 3 6 1.9505 - 1.8356 0.99 2706 137 0.1152 0.1536 REMARK 3 7 1.8356 - 1.7436 0.98 2698 140 0.1082 0.1374 REMARK 3 8 1.7436 - 1.6677 0.98 2675 128 0.1065 0.1197 REMARK 3 9 1.6677 - 1.6035 0.98 2664 126 0.1007 0.1359 REMARK 3 10 1.6035 - 1.5482 0.97 2632 156 0.1010 0.1184 REMARK 3 11 1.5482 - 1.4998 0.97 2627 136 0.0967 0.1426 REMARK 3 12 1.4998 - 1.4569 0.96 2576 148 0.1009 0.1450 REMARK 3 13 1.4569 - 1.4186 0.96 2601 146 0.1066 0.1398 REMARK 3 14 1.4186 - 1.3840 0.95 2554 150 0.1120 0.1355 REMARK 3 15 1.3840 - 1.3525 0.93 2523 128 0.1192 0.1531 REMARK 3 16 1.3525 - 1.3237 0.93 2508 108 0.1161 0.1689 REMARK 3 17 1.3237 - 1.2972 0.91 2471 143 0.1197 0.1732 REMARK 3 18 1.2972 - 1.2727 0.90 2437 108 0.1303 0.1841 REMARK 3 19 1.2727 - 1.2500 0.88 2373 139 0.1382 0.1978 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 : 0.44 REMARK 3 B_SOL : 46.40 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.82170 REMARK 3 B22 (A**2) : 0.95700 REMARK 3 B33 (A**2) : -0.13540 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 : 0.010 1428 REMARK 3 ANGLE : 1.307 1925 REMARK 3 CHIRALITY : 0.082 194 REMARK 3 PLANARITY : 0.006 260 REMARK 3 DIHEDRAL : 14.858 524 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 3K0M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-SEP-09. REMARK 100 THE DEPOSITION ID IS D_1000055395. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUN-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.953695 REMARK 200 MONOCHROMATOR : SIDE-SCATTERING CUBEROOT I-BEAM REMARK 200 BENT SINGLE CRYSTAL; ASYMETRIC REMARK 200 CUT 12.2 DEGS. REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54771 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04200 REMARK 200 FOR THE DATA SET : 38.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.56400 REMARK 200 FOR SHELL : 3.600 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: PDB ENTRY 2CPL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES PH 7.5, 22% PEG 3350, 5 REMARK 280 MM TCEP, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 21.20950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.31950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.87050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.31950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.20950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.87050 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 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 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 VAL A 2 CG1 CG2 REMARK 470 GLU A 165 CG CD OE1 OE2 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 O HOH A 217 O HOH A 218 2.16 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 PHE A 60 -77.00 -153.40 REMARK 500 PHE A 60 -76.19 -136.73 REMARK 500 ASN A 71 6.83 -151.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3K0N RELATED DB: PDB REMARK 900 RELATED ID: 3K0O RELATED DB: PDB REMARK 900 RELATED ID: 3K0P RELATED DB: PDB REMARK 900 RELATED ID: 3K0Q RELATED DB: PDB REMARK 900 RELATED ID: 3K0R RELATED DB: PDB DBREF 3K0M A 1 165 UNP P62937 PPIA_HUMAN 1 165 SEQRES 1 A 165 MET VAL ASN PRO THR VAL PHE PHE ASP ILE ALA VAL ASP SEQRES 2 A 165 GLY GLU PRO LEU GLY ARG VAL SER PHE GLU LEU PHE ALA SEQRES 3 A 165 ASP LYS VAL PRO LYS THR ALA GLU ASN PHE ARG ALA LEU SEQRES 4 A 165 SER THR GLY GLU LYS GLY PHE GLY TYR LYS GLY SER CYS SEQRES 5 A 165 PHE HIS ARG ILE ILE PRO GLY PHE MET CYS GLN GLY GLY SEQRES 6 A 165 ASP PHE THR ARG HIS ASN GLY THR GLY GLY LYS SER ILE SEQRES 7 A 165 TYR GLY GLU LYS PHE GLU ASP GLU ASN PHE ILE LEU LYS SEQRES 8 A 165 HIS THR GLY PRO GLY ILE LEU SER MET ALA ASN ALA GLY SEQRES 9 A 165 PRO ASN THR ASN GLY SER GLN PHE PHE ILE CYS THR ALA SEQRES 10 A 165 LYS THR GLU TRP LEU ASP GLY LYS HIS VAL VAL PHE GLY SEQRES 11 A 165 LYS VAL LYS GLU GLY MET ASN ILE VAL GLU ALA MET GLU SEQRES 12 A 165 ARG PHE GLY SER ARG ASN GLY LYS THR SER LYS LYS ILE SEQRES 13 A 165 THR ILE ALA ASP CYS GLY GLN LEU GLU FORMUL 2 HOH *269(H2 O) HELIX 1 1 VAL A 29 GLY A 42 1 14 HELIX 2 2 THR A 119 ASP A 123 5 5 HELIX 3 3 GLY A 135 ARG A 144 1 10 SHEET 1 A 8 PHE A 53 ILE A 57 0 SHEET 2 A 8 MET A 61 GLY A 64 -1 O GLN A 63 N ARG A 55 SHEET 3 A 8 PHE A 112 CYS A 115 -1 O ILE A 114 N CYS A 62 SHEET 4 A 8 ILE A 97 MET A 100 -1 N SER A 99 O PHE A 113 SHEET 5 A 8 VAL A 128 GLU A 134 -1 O GLY A 130 N LEU A 98 SHEET 6 A 8 GLU A 15 LEU A 24 -1 N SER A 21 O LYS A 133 SHEET 7 A 8 THR A 5 VAL A 12 -1 N ILE A 10 O GLY A 18 SHEET 8 A 8 ILE A 156 LEU A 164 -1 O ASP A 160 N ASP A 9 CRYST1 42.419 51.741 88.639 90.00 90.00 90.00 P 21 21 21 4 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 0.023574 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019327 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011282 0.00000