HEADER ISOMERASE 11-FEB-20 6LXR TITLE TVCYP2 IN APO FORM 4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYCLOPHILIN A PROTEIN, PPIASE; COMPND 5 EC: 5.2.1.8; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRICHOMONAS VAGINALIS; SOURCE 3 ORGANISM_TAXID: 5722; SOURCE 4 GENE: TVAG_062520; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.ARYAL,C.CHEN,C.H.HSU REVDAT 2 29-NOV-23 6LXR 1 REMARK REVDAT 1 09-SEP-20 6LXR 0 JRNL AUTH S.ARYAL,H.M.HSU,Y.C.LOU,C.H.CHU,J.H.TAI,C.H.HSU,C.CHEN JRNL TITL N-TERMINAL SEGMENT OF TVCYP2 CYCLOPHILIN FROMTRICHOMONAS JRNL TITL 2 VAGINALISIS INVOLVED IN SELF-ASSOCIATION, MEMBRANE JRNL TITL 3 INTERACTION, AND SUBCELLULAR LOCALIZATION. JRNL REF BIOMOLECULES V. 10 2020 JRNL REFN ESSN 2218-273X JRNL PMID 32859063 JRNL DOI 10.3390/BIOM10091239 REMARK 2 REMARK 2 RESOLUTION. 2.56 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 2.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.8 REMARK 3 NUMBER OF REFLECTIONS : 5340 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.980 REMARK 3 FREE R VALUE TEST SET COUNT : 533 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 4.0600 - 3.2300 1.00 1300 142 0.1711 0.2372 REMARK 3 2 3.2300 - 2.8200 0.99 1268 145 0.1997 0.2757 REMARK 3 3 26.1700 - 2.5610 1.00 1375 150 0.1437 0.1979 REMARK 3 4 2.8200 - 2.5600 0.68 864 96 0.2040 0.2766 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.787 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.61 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.84 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 : 0.008 1397 REMARK 3 ANGLE : 0.874 1879 REMARK 3 CHIRALITY : 0.059 203 REMARK 3 PLANARITY : 0.007 243 REMARK 3 DIHEDRAL : 3.534 824 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 6LXR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1300014877. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAY-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13C1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97622 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5340 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.560 REMARK 200 RESOLUTION RANGE LOW (A) : 26.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.56 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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 : 3.200 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: 5YBA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0 M SODIUM CITRATE, 0.2 M SODIUM REMARK 280 CHLORIDE, 0.1 M TRIS PH 7.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 283K 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 26.03950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.83550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.26950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.83550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.03950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.26950 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 LEU A 2 REMARK 465 ALA A 3 REMARK 465 PHE A 4 REMARK 465 LEU A 187 REMARK 465 GLU A 188 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 ALA A 121 O HOH A 201 2.11 REMARK 500 O GLY A 100 O HOH A 202 2.14 REMARK 500 OE1 GLU A 56 O HOH A 203 2.15 REMARK 500 NZ LYS A 14 OD2 ASP A 40 2.15 REMARK 500 OE2 GLU A 96 O HOH A 204 2.16 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 OD1 ASP A 41 OH TYR A 93 2665 2.18 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 80 -87.15 -145.42 REMARK 500 THR A 88 -83.88 -100.46 REMARK 500 REMARK 500 REMARK: NULL DBREF 6LXR A 1 186 UNP A2DLL4 A2DLL4_TRIVA 1 186 SEQADV 6LXR LEU A 187 UNP A2DLL4 EXPRESSION TAG SEQADV 6LXR GLU A 188 UNP A2DLL4 EXPRESSION TAG SEQRES 1 A 188 MET LEU ALA PHE PHE ALA THR ARG VAL ILE SER ALA PRO SEQRES 2 A 188 LYS VAL THR LYS LYS VAL PHE PHE LYS ILE SER ILE ASN SEQRES 3 A 188 GLY GLU ASP ALA GLY THR ILE LYS PHE GLY LEU PHE GLY SEQRES 4 A 188 ASP ASP VAL PRO LYS THR ALA GLU ASN PHE ARG ALA LEU SEQRES 5 A 188 CYS THR GLY GLU LYS GLY MET GLY LYS LEU GLY LYS PRO SEQRES 6 A 188 LEU HIS TYR LYS GLY SER PRO PHE HIS ARG VAL ILE PRO SEQRES 7 A 188 ASN PHE MET ILE GLN GLY GLY ASP ILE THR SER GLY ASN SEQRES 8 A 188 GLY TYR GLY GLY GLU SER ILE TYR GLY SER LYS PHE ALA SEQRES 9 A 188 ASP GLU SER PHE LYS ILE THR HIS ASP GLY PRO GLY LEU SEQRES 10 A 188 LEU SER MET ALA ASN SER GLY PRO ASN THR ASN GLY SER SEQRES 11 A 188 GLN PHE PHE ILE THR THR VAL PRO CYS PRO TRP LEU ASN SEQRES 12 A 188 GLY LYS HIS VAL VAL PHE GLY LYS VAL ILE GLU GLY MET SEQRES 13 A 188 GLU ILE VAL LYS LYS ILE GLU SER LEU GLY SER GLN SER SEQRES 14 A 188 GLY THR PRO LYS ALA LYS ILE ILE ILE ALA ASP CYS GLY SEQRES 15 A 188 GLU ILE THR GLU LEU GLU FORMUL 2 HOH *22(H2 O) HELIX 1 AA1 VAL A 42 GLY A 55 1 14 HELIX 2 AA2 CYS A 139 ASN A 143 5 5 HELIX 3 AA3 GLY A 155 LEU A 165 1 11 SHEET 1 AA1 8 ARG A 75 ILE A 77 0 SHEET 2 AA1 8 MET A 81 GLY A 84 -1 O MET A 81 N ILE A 77 SHEET 3 AA1 8 PHE A 132 THR A 135 -1 O ILE A 134 N ILE A 82 SHEET 4 AA1 8 LEU A 117 MET A 120 -1 N SER A 119 O PHE A 133 SHEET 5 AA1 8 VAL A 148 GLU A 154 -1 O GLY A 150 N LEU A 118 SHEET 6 AA1 8 GLU A 28 LEU A 37 -1 N LYS A 34 O ILE A 153 SHEET 7 AA1 8 VAL A 19 ILE A 25 -1 N ILE A 23 O ALA A 30 SHEET 8 AA1 8 ILE A 176 GLU A 183 -1 O ASP A 180 N LYS A 22 CRYST1 52.079 54.539 59.671 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 0.019202 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018336 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016759 0.00000