PDB Short entry for 6U5G HEADER ISOMERASE 27-AUG-19 6U5G TITLE MICROED STRUCTURE OF A FIB-MILLED CYPA CRYSTAL COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PPIASE A,CYCLOPHILIN A,CYCLOSPORIN A-BINDING PROTEIN, COMPND 5 ROTAMASE A; 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PEPTIDYL-PROLYL, CIS-TRANS, ISOMERASE, CYCLOPHILIN EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR A.M.WOLFF,M.W.MARTYNOWYCZ,W.ZHAO,T.GONEN,J.S.FRASER,M.C.THOMPSON REVDAT 4 11-OCT-23 6U5G 1 REMARK REVDAT 3 11-MAR-20 6U5G 1 JRNL REVDAT 2 12-FEB-20 6U5G 1 AUTHOR JRNL REVDAT 1 29-JAN-20 6U5G 0 JRNL AUTH A.M.WOLFF,I.D.YOUNG,R.G.SIERRA,A.S.BREWSTER,M.W.MARTYNOWYCZ, JRNL AUTH 2 E.NANGO,M.SUGAHARA,T.NAKANE,K.ITO,A.AQUILA,A.BHOWMICK, JRNL AUTH 3 J.T.BIEL,S.CARBAJO,A.E.COHEN,S.CORTEZ,A.GONZALEZ,T.HINO, JRNL AUTH 4 D.IM,J.D.KORALEK,M.KUBO,T.S.LAZAROU,T.NOMURA,S.OWADA, JRNL AUTH 5 A.SAMELSON,T.TANAKA,R.TANAKA,E.M.THOMPSON,H.VAN DEN BEDEM, JRNL AUTH 6 R.A.WOLDEYES,F.YUMOTO,W.ZHAO,K.TONO,S.BOUTET,S.IWATA, JRNL AUTH 7 T.GONEN,N.K.SAUTER,J.S.FRASER,M.C.THOMPSON JRNL TITL COMPARING SERIAL X-RAY CRYSTALLOGRAPHY AND MICROCRYSTAL JRNL TITL 2 ELECTRON DIFFRACTION (MICROED) AS METHODS FOR ROUTINE JRNL TITL 3 STRUCTURE DETERMINATION FROM SMALL MACROMOLECULAR CRYSTALS JRNL REF IUCRJ V. 7 306 2020 JRNL REFN ESSN 2052-2525 JRNL DOI 10.1107/S205225252000072X REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.0 REMARK 3 NUMBER OF REFLECTIONS : 11440 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.460 REMARK 3 FREE R VALUE TEST SET COUNT : 396 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 26.4800 - 3.6000 0.84 3582 122 0.1461 0.1548 REMARK 3 2 3.6000 - 2.8600 0.87 3717 141 0.2033 0.2848 REMARK 3 3 2.8600 - 2.5000 0.87 3745 133 0.2665 0.3217 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.422 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.539 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.52 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.60 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 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 1276 REMARK 3 ANGLE : 0.732 1711 REMARK 3 CHIRALITY : 0.055 177 REMARK 3 PLANARITY : 0.005 226 REMARK 3 DIHEDRAL : 12.819 744 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 6U5G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1000243874. REMARK 240 REMARK 240 EXPERIMENTAL DETAILS REMARK 240 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY REMARK 240 SAMPLE TYPE : 3D ARRAY REMARK 240 SPECIMEN TYPE : NULL REMARK 240 DATA ACQUISITION REMARK 240 DATE OF DATA COLLECTION : NULL REMARK 240 TEMPERATURE (KELVIN) : NULL REMARK 240 PH : NULL REMARK 240 NUMBER OF CRYSTALS USED : NULL REMARK 240 MICROSCOPE MODEL : FEI TALOS ARCTICA REMARK 240 DETECTOR TYPE : TVIPS TEMCAM-F416 (4K X 4K) REMARK 240 ACCELERATION VOLTAGE (KV) : 200 REMARK 240 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 240 RESOLUTION RANGE HIGH (A) : NULL REMARK 240 RESOLUTION RANGE LOW (A) : NULL REMARK 240 DATA SCALING SOFTWARE : XDS REMARK 240 COMPLETENESS FOR RANGE (%) : NULL REMARK 240 DATA REDUNDANCY : NULL REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :NULL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :NULL REMARK 240 COMPLETENESS FOR SHELL (%) : NULL REMARK 240 DATA REDUNDANCY IN SHELL : NULL REMARK 240 R MERGE FOR SHELL (I) : NULL REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 240 SOFTWARE USED : PHASER REMARK 240 STARTING MODEL : PDB ENTRY 4YUM 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 21.20000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.88000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.70000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.88000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.20000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.70000 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 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 GLU A 165 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 HD22 ASN A 35 O HOH A 206 1.51 REMARK 500 O ASP A 123 O HOH A 201 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 161 CB CYS A 161 SG -0.162 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 -76.24 -131.72 REMARK 500 HIS A 70 16.25 56.51 REMARK 500 THR A 107 26.32 -142.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-20645 RELATED DB: EMDB REMARK 900 MICROED STRUCTURE OF A FIB-MILLED CYPA CRYSTAL DBREF 6U5G 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 *32(H2 O) HELIX 1 AA1 VAL A 29 GLY A 42 1 14 HELIX 2 AA2 THR A 119 ASP A 123 5 5 HELIX 3 AA3 GLY A 135 ARG A 144 1 10 SHEET 1 AA1 8 ARG A 55 ILE A 57 0 SHEET 2 AA1 8 MET A 61 GLY A 64 -1 O GLN A 63 N ARG A 55 SHEET 3 AA1 8 PHE A 112 CYS A 115 -1 O ILE A 114 N CYS A 62 SHEET 4 AA1 8 ILE A 97 MET A 100 -1 N SER A 99 O PHE A 113 SHEET 5 AA1 8 VAL A 128 GLU A 134 -1 O GLY A 130 N LEU A 98 SHEET 6 AA1 8 GLU A 15 LEU A 24 -1 N SER A 21 O LYS A 133 SHEET 7 AA1 8 THR A 5 VAL A 12 -1 N PHE A 8 O VAL A 20 SHEET 8 AA1 8 ILE A 156 GLN A 163 -1 O ASP A 160 N ASP A 9 CRYST1 42.400 53.400 87.760 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 0.023585 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018727 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011395 0.00000