HEADER PROTEIN BINDING 12-APR-24 8Z28 TITLE FK506-BINDING PROTEIN 1B COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYLPROLYL ISOMERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: FK506 BINDING PROTEIN; 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 BINDING PROTEIN, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR X.H.LIU,W.H.ZHAO REVDAT 1 03-JUL-24 8Z28 0 JRNL AUTH X.H.LIU,W.H.ZHAO JRNL TITL FK506-BINDING PROTEIN 1B JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.35 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 51034 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 2560 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 34.0400 - 3.5400 1.00 2888 173 0.1534 0.1838 REMARK 3 2 3.5400 - 2.8100 1.00 2792 140 0.1624 0.1972 REMARK 3 3 2.8100 - 2.4500 1.00 2753 149 0.1749 0.1711 REMARK 3 4 2.4500 - 2.2300 1.00 2707 154 0.1595 0.1823 REMARK 3 5 2.2300 - 2.0700 0.99 2734 121 0.1442 0.1599 REMARK 3 6 2.0700 - 1.9500 0.99 2667 159 0.1452 0.1742 REMARK 3 7 1.9500 - 1.8500 0.99 2681 148 0.1591 0.1839 REMARK 3 8 1.8500 - 1.7700 0.99 2673 140 0.1665 0.1855 REMARK 3 9 1.7700 - 1.7000 0.99 2678 134 0.1585 0.1959 REMARK 3 10 1.7000 - 1.6400 0.99 2663 122 0.1561 0.2050 REMARK 3 11 1.6400 - 1.5900 0.99 2649 149 0.1451 0.1779 REMARK 3 12 1.5900 - 1.5500 0.99 2631 150 0.1425 0.1782 REMARK 3 13 1.5500 - 1.5000 0.99 2704 126 0.1491 0.1966 REMARK 3 14 1.5000 - 1.4700 0.99 2666 150 0.1646 0.2068 REMARK 3 15 1.4700 - 1.4300 0.99 2658 149 0.1607 0.1860 REMARK 3 16 1.4300 - 1.4000 0.99 2643 143 0.1562 0.1914 REMARK 3 17 1.4000 - 1.3800 0.99 2672 120 0.1661 0.2155 REMARK 3 18 1.3800 - 1.3500 0.98 2615 133 0.1726 0.2125 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.372 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.12 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.47 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 : 0.005 1736 REMARK 3 ANGLE : 0.897 2354 REMARK 3 CHIRALITY : 0.088 262 REMARK 3 PLANARITY : 0.007 310 REMARK 3 DIHEDRAL : 6.718 244 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 8Z28 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_1300046850. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-23 REMARK 200 TEMPERATURE (KELVIN) : 291.15 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 : 51043 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 34.040 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 11.70 REMARK 200 R MERGE (I) : 0.05233 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.0200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.29380 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.580 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 (%): 48.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4%V/V TACSIMATETM PH 8.0,12% W/V REMARK 280 POLYETHYLENE GLYCOL3,350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 27.72650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.03600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.53300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.03600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.72650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.53300 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 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 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 286 O HOH A 347 2.05 REMARK 500 O HOH A 264 O HOH A 317 2.14 REMARK 500 O HOH A 339 O HOH A 367 2.14 REMARK 500 O THR A 33 O HOH A 201 2.18 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 O HOH B 326 O HOH B 329 3644 2.19 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 ALA A 96 -46.68 -139.72 REMARK 500 ASP B 37 19.64 56.89 REMARK 500 ARG B 49 -140.84 -89.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 384 DISTANCE = 5.81 ANGSTROMS DBREF1 8Z28 A 1 113 UNP A0A4P7N8E2_PYROR DBREF2 8Z28 A A0A4P7N8E2 1 113 DBREF1 8Z28 B 1 113 UNP A0A4P7N8E2_PYROR DBREF2 8Z28 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 FORMUL 3 HOH *366(H2 O) HELIX 1 AA1 LYS A 35 ASP A 37 5 3 HELIX 2 AA2 ILE A 62 VAL A 70 1 9 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 ASP B 81 N THR B 4 SHEET 3 AA3 5 LEU B 103 ILE B 112 -1 O VAL B 107 N ALA B 78 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 GLY B 40 N LEU B 30 SHEET 1 AA4 5 VAL B 3 GLN B 9 0 SHEET 2 AA4 5 LYS B 77 ILE B 82 -1 O ASP B 81 N THR B 4 SHEET 3 AA4 5 LEU B 103 ILE B 112 -1 O VAL B 107 N ALA B 78 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 55.453 61.066 68.072 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 0.018033 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016376 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014690 0.00000