HEADER PROTEIN BINDING 14-APR-24 8Z38 TITLE FK506 BINDING PROTEIN 1B (INCLUDING FK506) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYLPROLYL ISOMERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: FK506 BINDING PROTEIN 1B(INCLUDING FK506); COMPND 5 EC: 5.2.1.8; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYRICULARIA ORYZAE; SOURCE 3 ORGANISM_TAXID: 318829; SOURCE 4 GENE: POMZ_03707; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FK506, FK506 BINDING PROTEIN 1B, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR X.H.LIU,W.H.ZHAO REVDAT 1 03-JUL-24 8Z38 0 JRNL AUTH X.H.LIU,W.H.ZHAO JRNL TITL HIGH-RESOLUTION COCRYSTALLIZED CRYSTAL STRUCTURES OF FK506 JRNL TITL 2 AND FK506-BINDING PROTEINS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.17 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.17 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.9 REMARK 3 NUMBER OF REFLECTIONS : 10841 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.820 REMARK 3 FREE R VALUE TEST SET COUNT : 522 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 42.6500 - 3.4400 0.86 2579 138 0.1652 0.2252 REMARK 3 2 3.4400 - 2.7300 0.86 2485 139 0.2013 0.2501 REMARK 3 3 2.7300 - 2.3900 0.92 2619 121 0.2538 0.3421 REMARK 3 4 2.3900 - 2.1700 0.92 2636 124 0.2383 0.2988 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.262 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.41 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.64 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 : 0.006 1721 REMARK 3 ANGLE : 0.828 2329 REMARK 3 CHIRALITY : 0.055 258 REMARK 3 PLANARITY : 0.006 306 REMARK 3 DIHEDRAL : 13.281 631 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 8Z38 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-APR-24. REMARK 100 THE DEPOSITION ID IS D_1300046890. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-SEP-23 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 : SSRF REMARK 200 BEAMLINE : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 7.21 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 7.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10844 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.170 REMARK 200 RESOLUTION RANGE LOW (A) : 42.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.9 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.17120 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.7400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.17 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.25 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.72580 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.7.0 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5, 1.4 M TRI-SODIUM REMARK 280 CITRATE DIHYDRATE OR 2.1 M DL-MALIC ACID PH 7.0., VAPOR REMARK 280 DIFFUSION, HANGING 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 27.57850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.62300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.69100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.62300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.57850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.69100 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: 1940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 MET A 1 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 332 O HOH A 343 1.99 REMARK 500 O VAL A 70 O HOH A 301 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 SER A 45 137.34 -171.91 REMARK 500 ALA A 96 -50.88 -127.63 REMARK 500 SER B 34 30.34 -94.23 REMARK 500 ASP B 37 14.66 59.25 REMARK 500 ARG B 49 -163.49 -126.70 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8Z38 A 1 113 UNP A0A4P7N8E2_PYROR DBREF2 8Z38 A A0A4P7N8E2 1 113 DBREF1 8Z38 B 1 113 UNP A0A4P7N8E2_PYROR DBREF2 8Z38 B A0A4P7N8E2 1 113 SEQRES 1 A 113 MET GLY VAL THR LYS THR THR THR GLN GLN GLY THR GLY SEQRES 2 A 113 PRO SER PRO GLN VAL GLY GLN THR VAL VAL ILE GLU TYR SEQRES 3 A 113 THR GLY PHE LEU LYS ASP THR SER LYS PRO ASP ASN LYS SEQRES 4 A 113 GLY ALA GLN PHE ASP SER SER VAL GLY ARG GLY ASP PHE SEQRES 5 A 113 GLU THR ALA ILE GLY VAL GLN ARG VAL ILE LYS GLY TRP SEQRES 6 A 113 ASP GLU GLY VAL VAL SER MET LYS VAL GLY GLU LYS ALA SEQRES 7 A 113 THR LEU ASP ILE THR ALA ASP TYR GLY TYR GLY ALA ARG SEQRES 8 A 113 GLY PHE PRO GLY ALA ILE PRO PRO ASN SER ASP LEU ILE SEQRES 9 A 113 PHE ASP VAL TYR LEU LYS GLY ILE LYS SEQRES 1 B 113 MET GLY VAL THR LYS THR THR THR GLN GLN GLY THR GLY SEQRES 2 B 113 PRO SER PRO GLN VAL GLY GLN THR VAL VAL ILE GLU TYR SEQRES 3 B 113 THR GLY PHE LEU LYS ASP THR SER LYS PRO ASP ASN LYS SEQRES 4 B 113 GLY ALA GLN PHE ASP SER SER VAL GLY ARG GLY ASP PHE SEQRES 5 B 113 GLU THR ALA ILE GLY VAL GLN ARG VAL ILE LYS GLY TRP SEQRES 6 B 113 ASP GLU GLY VAL VAL SER MET LYS VAL GLY GLU LYS ALA SEQRES 7 B 113 THR LEU ASP ILE THR ALA ASP TYR GLY TYR GLY ALA ARG SEQRES 8 B 113 GLY PHE PRO GLY ALA ILE PRO PRO ASN SER ASP LEU ILE SEQRES 9 B 113 PHE ASP VAL TYR LEU LYS GLY ILE LYS HET CPI A 201 9 HETNAM CPI 6-CARBOXYPIPERIDINE FORMUL 3 CPI C6 H11 N O2 FORMUL 4 HOH *76(H2 O) HELIX 1 AA1 LYS A 35 ASP A 37 5 3 HELIX 2 AA2 ILE A 62 SER A 71 1 10 HELIX 3 AA3 ALA A 84 GLY A 87 5 4 HELIX 4 AA4 LYS B 35 ASP B 37 5 3 HELIX 5 AA5 ILE B 62 SER B 71 1 10 HELIX 6 AA6 ALA B 84 GLY B 87 5 4 SHEET 1 AA1 5 VAL A 3 GLN A 9 0 SHEET 2 AA1 5 LYS A 77 ILE A 82 -1 O ASP A 81 N THR A 4 SHEET 3 AA1 5 LEU A 103 ILE A 112 -1 O VAL A 107 N ALA A 78 SHEET 4 AA1 5 THR A 21 LYS A 31 -1 N PHE A 29 O ILE A 104 SHEET 5 AA1 5 LYS A 39 SER A 45 -1 O ASP A 44 N GLY A 28 SHEET 1 AA2 5 VAL A 3 GLN A 9 0 SHEET 2 AA2 5 LYS A 77 ILE A 82 -1 O ASP A 81 N THR A 4 SHEET 3 AA2 5 LEU A 103 ILE A 112 -1 O VAL A 107 N ALA A 78 SHEET 4 AA2 5 THR A 21 LYS A 31 -1 N PHE A 29 O ILE A 104 SHEET 5 AA2 5 PHE A 52 ALA A 55 -1 O THR A 54 N VAL A 22 SHEET 1 AA3 5 VAL B 3 GLN B 9 0 SHEET 2 AA3 5 LYS B 77 ILE B 82 -1 O THR B 79 N THR B 6 SHEET 3 AA3 5 LEU B 103 ILE B 112 -1 O LEU B 103 N ILE B 82 SHEET 4 AA3 5 THR B 21 LYS B 31 -1 N PHE B 29 O ILE B 104 SHEET 5 AA3 5 LYS B 39 SER B 45 -1 O ASP B 44 N GLY B 28 SHEET 1 AA4 5 VAL B 3 GLN B 9 0 SHEET 2 AA4 5 LYS B 77 ILE B 82 -1 O THR B 79 N THR B 6 SHEET 3 AA4 5 LEU B 103 ILE B 112 -1 O LEU B 103 N ILE B 82 SHEET 4 AA4 5 THR B 21 LYS B 31 -1 N PHE B 29 O ILE B 104 SHEET 5 AA4 5 PHE B 52 ALA B 55 -1 O THR B 54 N VAL B 22 CRYST1 55.157 59.382 67.246 90.00 90.00 90.00 P 21 21 21 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 0.018130 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016840 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014871 0.00000