HEADER ISOMERASE 05-MAY-22 7UXN TITLE STRUCTURE OF PPIA IN COMPLEX WITH FP29103, A HELICON POLYPEPTIDE 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; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: FP29103; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: STAPLED PEPTIDE 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; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS COMPLEX, STAPLED, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR K.LI,S.AGARWAL,O.TOKAREVA,T.THOMSON,H.TATTERSFIELD,S.WAHL,G.VERDINE, AUTHOR 2 J.MCGEE REVDAT 3 06-NOV-24 7UXN 1 REMARK REVDAT 2 25-OCT-23 7UXN 1 REMARK REVDAT 1 28-DEC-22 7UXN 0 JRNL AUTH K.LI,O.S.TOKAREVA,T.M.THOMSON,S.C.T.WAHL,T.L.TRAVALINE, JRNL AUTH 2 J.D.RAMIREZ,S.K.CHOUDARY,S.AGARWAL,W.G.WALKUP 4TH,T.J.OLSEN, JRNL AUTH 3 M.J.BRENNAN,G.L.VERDINE,J.H.MCGEE JRNL TITL DE NOVO MAPPING OF ALPHA-HELIX RECOGNITION SITES ON PROTEIN JRNL TITL 2 SURFACES USING UNBIASED LIBRARIES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 119 35119 2022 JRNL REFN ESSN 1091-6490 JRNL PMID 36534810 JRNL DOI 10.1073/PNAS.2210435119 REMARK 2 REMARK 2 RESOLUTION. 1.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 1.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 36286 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.510 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 41.4100 - 3.2800 1.00 2638 154 0.1619 0.1838 REMARK 3 2 3.2800 - 2.6000 1.00 2510 147 0.1904 0.2085 REMARK 3 3 2.6000 - 2.2700 1.00 2479 144 0.1963 0.2201 REMARK 3 4 2.2700 - 2.0600 1.00 2465 143 0.1978 0.2208 REMARK 3 5 2.0600 - 1.9200 1.00 2442 143 0.2068 0.2408 REMARK 3 6 1.9200 - 1.8000 1.00 2454 144 0.2026 0.2255 REMARK 3 7 1.8000 - 1.7100 1.00 2442 142 0.2029 0.2575 REMARK 3 8 1.7100 - 1.6400 1.00 2417 140 0.2111 0.2353 REMARK 3 9 1.6400 - 1.5800 1.00 2456 144 0.2181 0.2332 REMARK 3 10 1.5800 - 1.5200 1.00 2406 140 0.2129 0.2446 REMARK 3 11 1.5200 - 1.4700 1.00 2437 142 0.2271 0.2406 REMARK 3 12 1.4700 - 1.4300 1.00 2419 141 0.2380 0.2716 REMARK 3 13 1.4300 - 1.3900 1.00 2406 141 0.2697 0.2671 REMARK 3 14 1.3900 - 1.3600 0.96 2315 135 0.2995 0.3105 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.740 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.36 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7UXN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1000265144. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAY-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97741 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36286 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.360 REMARK 200 RESOLUTION RANGE LOW (A) : 41.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 12.30 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.41 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.95100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 3K0N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM ACETATE, 0.1 M SODIUM REMARK 280 CACODYLATE PH 6.5, 30% W/V PEG 8000., VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 291.15K 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 21.04000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.93500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.00500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.93500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.04000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.00500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 GLY A 0 REMARK 465 MET A 1 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 -73.88 -126.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7UWI RELATED DB: PDB REMARK 900 RELATED ID: 7UWO RELATED DB: PDB DBREF 7UXN A 1 165 UNP P62937 PPIA_HUMAN 1 165 DBREF 7UXN B 0 11 PDB 7UXN 7UXN 0 11 SEQADV 7UXN GLY A 0 UNP P62937 EXPRESSION TAG SEQRES 1 A 166 GLY MET VAL ASN PRO THR VAL PHE PHE ASP ILE ALA VAL SEQRES 2 A 166 ASP GLY GLU PRO LEU GLY ARG VAL SER PHE GLU LEU PHE SEQRES 3 A 166 ALA ASP LYS VAL PRO LYS THR ALA GLU ASN PHE ARG ALA SEQRES 4 A 166 LEU SER THR GLY GLU LYS GLY PHE GLY TYR LYS GLY SER SEQRES 5 A 166 CYS PHE HIS ARG ILE ILE PRO GLY PHE MET CYS GLN GLY SEQRES 6 A 166 GLY ASP PHE THR ARG HIS ASN GLY THR GLY GLY LYS SER SEQRES 7 A 166 ILE TYR GLY GLU LYS PHE GLU ASP GLU ASN PHE ILE LEU SEQRES 8 A 166 LYS HIS THR GLY PRO GLY ILE LEU SER MET ALA ASN ALA SEQRES 9 A 166 GLY PRO ASN THR ASN GLY SER GLN PHE PHE ILE CYS THR SEQRES 10 A 166 ALA LYS THR GLU TRP LEU ASP GLY LYS HIS VAL VAL PHE SEQRES 11 A 166 GLY LYS VAL LYS GLU GLY MET ASN ILE VAL GLU ALA MET SEQRES 12 A 166 GLU ARG PHE GLY SER ARG ASN GLY LYS THR SER LYS LYS SEQRES 13 A 166 ILE THR ILE ALA ASP CYS GLY GLN LEU GLU SEQRES 1 B 12 ACE PRO ASP CYS HIS ILE ARG ALA TYR VAL CYS HIS HET ACE B 0 3 HET WHL B 101 14 HETNAM ACE ACETYL GROUP HETNAM WHL N,N'-(1,4-PHENYLENE)DIACETAMIDE FORMUL 2 ACE C2 H4 O FORMUL 3 WHL C10 H12 N2 O2 FORMUL 4 HOH *197(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 HELIX 4 AA4 ASP B 2 HIS B 11 1 10 SHEET 1 AA1 8 PHE A 53 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 ILE A 97 O CYS A 115 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 ILE A 10 O LEU A 17 SHEET 8 AA1 8 ILE A 156 GLN A 163 -1 O ASP A 160 N ASP A 9 LINK C ACE B 0 N PRO B 1 1555 1555 1.32 LINK SG CYS B 3 CH WHL B 101 1555 1555 1.71 LINK SG CYS B 10 CK WHL B 101 1555 1555 1.75 CRYST1 42.080 48.010 81.870 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 0.023764 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020829 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012214 0.00000