HEADER HYDROLASE 30-AUG-24 9GN7 TITLE CRYSTAL STRUCTURE OF DEACETYLASE (HDAH) FROM KLEBSIELLA PNEUMONIAE TITLE 2 SUBSP. OZAENAE IN COMPLEX WITH THE INHIBITOR TSA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEACETYLASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.5.1.-; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: HIS6-TGGED FUSION-PROTEIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE SUBSP. OZAENAE; SOURCE 3 ORGANISM_TAXID: 574; SOURCE 4 STRAIN: NCTC10313; SOURCE 5 GENE: HDAH, NCTC10313_02007, NCTC5050_05964; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET45-B(+) KEYWDS INHIBITOR, TSA, DEACETYLASE WITH TSA, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.QIN,L.G.GRAF,S.SCHULZE,G.J.PALM,M.LAMMERS REVDAT 2 13-NOV-24 9GN7 1 JRNL REVDAT 1 06-NOV-24 9GN7 0 JRNL AUTH L.G.GRAF,C.MORENO-YRUELA,C.QIN,S.SCHULZE,G.J.PALM, JRNL AUTH 2 O.SCHMOKER,N.WANG,D.M.HOCKING,L.JEBELI,B.GIRBARDT,L.BERNDT, JRNL AUTH 3 B.DORRE,D.M.WEIS,M.JANETZKY,D.ALBRECHT,D.ZUHLKE,S.SIEVERS, JRNL AUTH 4 R.A.STRUGNELL,C.A.OLSEN,K.HOFMANN,M.LAMMERS JRNL TITL DISTRIBUTION AND DIVERSITY OF CLASSICAL DEACYLASES IN JRNL TITL 2 BACTERIA. JRNL REF NAT COMMUN V. 15 9496 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 39489725 JRNL DOI 10.1038/S41467-024-53903-0 REMARK 2 REMARK 2 RESOLUTION. 2.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0425 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.39 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 27437 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.022 REMARK 3 FREE R VALUE TEST SET COUNT : 1378 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.18 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.24 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1919 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.2210 REMARK 3 BIN FREE R VALUE SET COUNT : 88 REMARK 3 BIN FREE R VALUE : 0.2390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2822 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 119 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.05 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.151 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.140 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.103 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.187 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2926 ; 0.014 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 2720 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3963 ; 2.236 ; 1.813 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6261 ; 0.756 ; 1.745 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 369 ; 6.855 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 28 ;11.793 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 457 ;14.005 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 422 ; 0.106 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3545 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 683 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 627 ; 0.246 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 95 ; 0.139 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1443 ; 0.191 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 106 ; 0.183 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 11 ; 0.210 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1479 ; 4.944 ; 4.003 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1479 ; 4.943 ; 4.003 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1847 ; 6.392 ; 7.149 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1848 ; 6.392 ; 7.154 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1447 ; 7.262 ; 4.601 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1448 ; 7.262 ; 4.603 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2116 ; 9.272 ; 8.127 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2117 ; 9.270 ; 8.128 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 9GN7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-AUG-24. REMARK 100 THE DEPOSITION ID IS D_1292141049. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-OCT-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS MAR 15, 2019 BUILT=20190315 REMARK 200 DATA SCALING SOFTWARE : XDS MAR 15, 2019 BUILT=20190315 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27454 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.180 REMARK 200 RESOLUTION RANGE LOW (A) : 47.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 1.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 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 : 2.500 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% (W/V) PEG 8000, 10% (V/V) GLYCEROL REMARK 280 AND 0.5M KCL, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X REMARK 290 13555 X+1/2,Y+1/2,Z+1/2 REMARK 290 14555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 15555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 16555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 17555 Z+1/2,X+1/2,Y+1/2 REMARK 290 18555 Z+1/2,-X+1/2,-Y+1/2 REMARK 290 19555 -Z+1/2,-X+1/2,Y+1/2 REMARK 290 20555 -Z+1/2,X+1/2,-Y+1/2 REMARK 290 21555 Y+1/2,Z+1/2,X+1/2 REMARK 290 22555 -Y+1/2,Z+1/2,-X+1/2 REMARK 290 23555 Y+1/2,-Z+1/2,-X+1/2 REMARK 290 24555 -Y+1/2,-Z+1/2,X+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 73.28500 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 73.28500 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 73.28500 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 73.28500 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 73.28500 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 73.28500 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 73.28500 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 73.28500 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 73.28500 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 73.28500 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 73.28500 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 73.28500 REMARK 290 SMTRY1 17 0.000000 0.000000 1.000000 73.28500 REMARK 290 SMTRY2 17 1.000000 0.000000 0.000000 73.28500 REMARK 290 SMTRY3 17 0.000000 1.000000 0.000000 73.28500 REMARK 290 SMTRY1 18 0.000000 0.000000 1.000000 73.28500 REMARK 290 SMTRY2 18 -1.000000 0.000000 0.000000 73.28500 REMARK 290 SMTRY3 18 0.000000 -1.000000 0.000000 73.28500 REMARK 290 SMTRY1 19 0.000000 0.000000 -1.000000 73.28500 REMARK 290 SMTRY2 19 -1.000000 0.000000 0.000000 73.28500 REMARK 290 SMTRY3 19 0.000000 1.000000 0.000000 73.28500 REMARK 290 SMTRY1 20 0.000000 0.000000 -1.000000 73.28500 REMARK 290 SMTRY2 20 1.000000 0.000000 0.000000 73.28500 REMARK 290 SMTRY3 20 0.000000 -1.000000 0.000000 73.28500 REMARK 290 SMTRY1 21 0.000000 1.000000 0.000000 73.28500 REMARK 290 SMTRY2 21 0.000000 0.000000 1.000000 73.28500 REMARK 290 SMTRY3 21 1.000000 0.000000 0.000000 73.28500 REMARK 290 SMTRY1 22 0.000000 -1.000000 0.000000 73.28500 REMARK 290 SMTRY2 22 0.000000 0.000000 1.000000 73.28500 REMARK 290 SMTRY3 22 -1.000000 0.000000 0.000000 73.28500 REMARK 290 SMTRY1 23 0.000000 1.000000 0.000000 73.28500 REMARK 290 SMTRY2 23 0.000000 0.000000 -1.000000 73.28500 REMARK 290 SMTRY3 23 -1.000000 0.000000 0.000000 73.28500 REMARK 290 SMTRY1 24 0.000000 -1.000000 0.000000 73.28500 REMARK 290 SMTRY2 24 0.000000 0.000000 -1.000000 73.28500 REMARK 290 SMTRY3 24 1.000000 0.000000 0.000000 73.28500 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 21700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 41780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -291.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 146.57000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 146.57000 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 -10 REMARK 465 ALA A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 VAL A -2 REMARK 465 GLY A -1 REMARK 465 THR A 0 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 HD1 HIS A 183 ZN ZN A 403 1.16 REMARK 500 HE21 GLN A 189 HH TYR A 213 1.27 REMARK 500 HH21 ARG A 256 O HOH A 503 1.58 REMARK 500 O HOH A 586 O HOH A 610 1.59 REMARK 500 O HOH A 555 O HOH A 611 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 ARG A 86 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 139 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 219 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 287 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 358 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES 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 THR A 18 16.02 -143.45 REMARK 500 VAL A 23 -102.76 62.80 REMARK 500 SER A 66 -160.10 -108.25 REMARK 500 LEU A 98 78.45 -106.51 REMARK 500 GLU A 101 72.28 36.03 REMARK 500 ALA A 102 78.70 -164.56 REMARK 500 ALA A 214 -66.11 -103.19 REMARK 500 CYS A 301 33.74 -143.79 REMARK 500 GLU A 310 -104.20 -116.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 219 0.09 SIDE CHAIN REMARK 500 ARG A 256 0.13 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 401 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 179 O REMARK 620 2 ASP A 179 OD1 69.6 REMARK 620 3 ASP A 181 O 98.5 87.6 REMARK 620 4 HIS A 183 O 168.9 99.3 81.6 REMARK 620 5 SER A 202 OG 89.7 116.3 156.0 94.6 REMARK 620 6 LEU A 203 O 76.1 138.7 75.0 114.5 85.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 181 OD1 REMARK 620 2 ASP A 181 OD2 58.0 REMARK 620 3 HIS A 183 ND1 99.2 155.8 REMARK 620 4 ASP A 269 OD2 106.5 88.7 90.8 REMARK 620 5 TSN A 405 O1 98.7 91.3 100.9 150.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 402 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 192 O REMARK 620 2 ARG A 195 O 78.2 REMARK 620 3 VAL A 198 O 131.2 82.7 REMARK 620 4 TYR A 227 O 148.1 114.4 80.6 REMARK 620 5 HOH A 541 O 65.8 137.6 138.1 88.6 REMARK 620 6 HOH A 584 O 77.3 79.5 141.9 76.6 71.6 REMARK 620 N 1 2 3 4 5 DBREF1 9GN7 A 1 371 UNP A0A377Z5F6_KLEPO DBREF2 9GN7 A A0A377Z5F6 1 371 SEQADV 9GN7 MET A -10 UNP A0A377Z5F INITIATING METHIONINE SEQADV 9GN7 ALA A -9 UNP A0A377Z5F EXPRESSION TAG SEQADV 9GN7 HIS A -8 UNP A0A377Z5F EXPRESSION TAG SEQADV 9GN7 HIS A -7 UNP A0A377Z5F EXPRESSION TAG SEQADV 9GN7 HIS A -6 UNP A0A377Z5F EXPRESSION TAG SEQADV 9GN7 HIS A -5 UNP A0A377Z5F EXPRESSION TAG SEQADV 9GN7 HIS A -4 UNP A0A377Z5F EXPRESSION TAG SEQADV 9GN7 HIS A -3 UNP A0A377Z5F EXPRESSION TAG SEQADV 9GN7 VAL A -2 UNP A0A377Z5F EXPRESSION TAG SEQADV 9GN7 GLY A -1 UNP A0A377Z5F EXPRESSION TAG SEQADV 9GN7 THR A 0 UNP A0A377Z5F EXPRESSION TAG SEQRES 1 A 382 MET ALA HIS HIS HIS HIS HIS HIS VAL GLY THR MET LYS SEQRES 2 A 382 ARG LYS THR GLY PHE PHE PHE ASP GLU ARG CYS PHE TRP SEQRES 3 A 382 HIS SER THR GLY LEU HIS ALA VAL THR LEU PRO VAL GLY SEQRES 4 A 382 GLY TRP VAL GLN PRO PRO ALA GLY GLY GLY HIS ALA GLU SEQRES 5 A 382 SER PRO GLU THR LYS ARG ARG MET LYS ASN LEU MET ASP SEQRES 6 A 382 VAL SER GLY LEU THR PRO GLN LEU ALA LEU ARG SER ALA SEQRES 7 A 382 ALA PRO ALA SER LEU GLU ASP LEU ARG ARG ILE HIS PRO SEQRES 8 A 382 ASP SER TYR LEU GLU ARG PHE LYS ALA ILE SER ASP ASN SEQRES 9 A 382 GLY GLY GLY MET LEU GLY LYS GLU ALA PRO LEU GLY PRO SEQRES 10 A 382 GLY SER TYR GLU ILE ALA CYS LEU SER ALA GLY LEU ALA SEQRES 11 A 382 CYS ALA ALA VAL GLU ALA VAL LEU LYS GLY GLU LEU ASP SEQRES 12 A 382 ASN ALA TYR SER LEU SER ARG PRO PRO GLY HIS HIS CYS SEQRES 13 A 382 LEU PRO ASP GLN SER MET GLY PHE CYS PHE LEU ALA ASN SEQRES 14 A 382 ILE PRO ILE ALA VAL GLU ARG ALA LYS ALA GLN LEU GLY SEQRES 15 A 382 LEU GLY LYS VAL ALA ILE ILE ASP TRP ASP VAL HIS HIS SEQRES 16 A 382 GLY ASN GLY THR GLN HIS ILE TYR LEU GLN ARG ASP ASP SEQRES 17 A 382 VAL LEU THR ILE SER LEU HIS GLN ASP GLY CYS PHE PRO SEQRES 18 A 382 PRO GLY TYR ALA GLY GLU ASP ASP ARG GLY VAL GLY ALA SEQRES 19 A 382 GLY GLU GLY TYR ASN ILE ASN ILE PRO LEU LEU ALA GLY SEQRES 20 A 382 ALA GLY ASP ASP SER TRP ARG TYR ALA LEU GLU THR ILE SEQRES 21 A 382 VAL ILE PRO ALA LEU ALA ARG PHE GLU PRO GLU LEU ILE SEQRES 22 A 382 ILE ILE ALA CYS GLY TYR ASP ALA ASN ALA MET ASP PRO SEQRES 23 A 382 LEU ALA ARG MET GLN LEU HIS SER ASP SER PHE ARG ALA SEQRES 24 A 382 MET THR GLU GLN VAL GLN GLN ALA ALA ASP ARG LEU CYS SEQRES 25 A 382 GLY GLY LYS LEU VAL MET VAL HIS GLU GLY GLY TYR ALA SEQRES 26 A 382 GLU SER TYR VAL PRO PHE CYS GLY LEU ALA VAL MET GLU SEQRES 27 A 382 ALA LEU SER GLY ILE ARG THR GLU VAL GLN ASP PRO LEU SEQRES 28 A 382 LEU GLU PHE ILE GLN GLN GLN GLN PRO ARG ALA THR PHE SEQRES 29 A 382 ALA GLN PHE GLN ARG GLN ALA ILE ASP ARG LEU ALA GLN SEQRES 30 A 382 GLN PHE GLY LEU GLN HET K A 401 1 HET K A 402 1 HET ZN A 403 1 HET PO4 A 404 5 HET TSN A 405 44 HET GOL A 406 14 HET GOL A 407 20 HETNAM K POTASSIUM ION HETNAM ZN ZINC ION HETNAM PO4 PHOSPHATE ION HETNAM TSN TRICHOSTATIN A HETNAM GOL GLYCEROL HETSYN TSN 7-[4-(DIMETHYLAMINO)PHENYL]-N-HYDROXY-4,6-DIMETHYL-7- HETSYN 2 TSN OXO-2,4-HEPTADIENAMIDE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 K 2(K 1+) FORMUL 4 ZN ZN 2+ FORMUL 5 PO4 O4 P 3- FORMUL 6 TSN C17 H22 N2 O3 FORMUL 7 GOL 2(C3 H8 O3) FORMUL 9 HOH *119(H2 O) HELIX 1 AA1 ASP A 10 HIS A 16 5 7 HELIX 2 AA2 PRO A 43 SER A 56 1 14 HELIX 3 AA3 LEU A 58 LEU A 62 5 5 HELIX 4 AA4 SER A 71 ARG A 77 1 7 HELIX 5 AA5 PRO A 80 ASN A 93 1 14 HELIX 6 AA6 GLY A 107 LYS A 128 1 22 HELIX 7 AA7 ALA A 157 LEU A 170 1 14 HELIX 8 AA8 GLY A 185 TYR A 192 1 8 HELIX 9 AA9 VAL A 221 GLU A 225 5 5 HELIX 10 AB1 GLY A 238 ILE A 249 1 12 HELIX 11 AB2 ILE A 249 GLU A 258 1 10 HELIX 12 AB3 HIS A 282 GLY A 302 1 21 HELIX 13 AB4 TYR A 317 GLY A 331 1 15 HELIX 14 AB5 LEU A 340 GLN A 347 1 8 HELIX 15 AB6 ARG A 350 PHE A 368 1 19 SHEET 1 AA1 8 ALA A 63 ARG A 65 0 SHEET 2 AA1 8 THR A 5 PHE A 8 1 N THR A 5 O ALA A 63 SHEET 3 AA1 8 ASN A 133 SER A 136 1 O TYR A 135 N PHE A 8 SHEET 4 AA1 8 LEU A 305 HIS A 309 1 O MET A 307 N ALA A 134 SHEET 5 AA1 8 ILE A 262 CYS A 266 1 N ILE A 264 O VAL A 306 SHEET 6 AA1 8 VAL A 175 ASP A 179 1 N ILE A 178 O ALA A 265 SHEET 7 AA1 8 VAL A 198 GLN A 205 1 O LEU A 199 N ILE A 177 SHEET 8 AA1 8 ASN A 228 LEU A 233 1 O ILE A 231 N SER A 202 SHEET 1 AA2 2 HIS A 21 ALA A 22 0 SHEET 2 AA2 2 LEU A 25 PRO A 26 -1 O LEU A 25 N ALA A 22 SHEET 1 AA3 2 GLY A 96 MET A 97 0 SHEET 2 AA3 2 PRO A 103 LEU A 104 -1 O LEU A 104 N GLY A 96 LINK O ASP A 179 K K A 401 1555 1555 2.84 LINK OD1 ASP A 179 K K A 401 1555 1555 2.59 LINK O ASP A 181 K K A 401 1555 1555 2.57 LINK OD1 ASP A 181 ZN ZN A 403 1555 1555 1.98 LINK OD2 ASP A 181 ZN ZN A 403 1555 1555 2.53 LINK O HIS A 183 K K A 401 1555 1555 2.62 LINK ND1 HIS A 183 ZN ZN A 403 1555 1555 2.03 LINK O TYR A 192 K K A 402 1555 1555 2.58 LINK O ARG A 195 K K A 402 1555 1555 2.97 LINK O VAL A 198 K K A 402 1555 1555 2.49 LINK OG SER A 202 K K A 401 1555 1555 2.86 LINK O LEU A 203 K K A 401 1555 1555 2.47 LINK O TYR A 227 K K A 402 1555 1555 3.06 LINK OD2 ASP A 269 ZN ZN A 403 1555 1555 2.00 LINK K K A 402 O HOH A 541 1555 1555 3.18 LINK K K A 402 O HOH A 584 1555 1555 2.48 LINK ZN ZN A 403 O1 TSN A 405 1555 1555 1.84 CISPEP 1 ARG A 139 PRO A 140 0 4.69 CISPEP 2 PHE A 209 PRO A 210 0 -7.48 CRYST1 146.570 146.570 146.570 90.00 90.00 90.00 I 2 3 24 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 0.006823 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006823 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006823 0.00000