HEADER HYDROLASE/HYDROLASE INHIBITOR 29-JUL-15 5CXJ TITLE STRUCTURE OF XOO1075, A PEPTIDE DEFORMYLASE FROM XANTHOMONAS ORYZAE PV TITLE 2 ORYZAE, IN COMPLEX WITH FRAGMENT 124 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE DEFORMYLASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 42-212; COMPND 5 SYNONYM: PDF,POLYPEPTIDE DEFORMYLASE; COMPND 6 EC: 3.5.1.88; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XANTHOMONAS ORYZAE PV. ORYZAE KACC10331; SOURCE 3 ORGANISM_TAXID: 291331; SOURCE 4 STRAIN: KACC10331; SOURCE 5 GENE: DEF, XOO1075; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS PEPTIDE DEFORMYLASE, XANTHOMONAS, FRAGMENT, METALLOPEPTIDASE, KEYWDS 2 HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.P.T.NGO,L.W.KANG REVDAT 2 08-NOV-23 5CXJ 1 REMARK LINK REVDAT 1 03-AUG-16 5CXJ 0 JRNL AUTH H.P.T.NGO,L.W.KANG JRNL TITL STRUCTURE OF XOO1075, A PEPTIDE DEFORMYLASE FROM XANTHOMONAS JRNL TITL 2 ORYZAE PV ORYZAE, IN COMPLEX WITH FRAGMENT 124 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 11142 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 554 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) : 2.38 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 815 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2320 REMARK 3 BIN FREE R VALUE SET COUNT : 34 REMARK 3 BIN FREE R VALUE : 0.3310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1262 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 17 REMARK 3 SOLVENT ATOMS : 104 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.04000 REMARK 3 B12 (A**2) : -0.01000 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): 0.220 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.193 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.125 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.332 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1310 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1770 ; 1.945 ; 1.974 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 159 ; 6.902 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 64 ;31.577 ;22.813 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 204 ;15.315 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;19.526 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 189 ; 0.135 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1021 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL 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): 642 ; 2.146 ; 2.555 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 799 ; 3.178 ; 3.799 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 667 ; 3.769 ; 2.887 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2004 ; 6.794 ;22.354 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 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 5CXJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212324. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-DEC-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11794 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.380 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: HKL-2000 REMARK 200 STARTING MODEL: 5E5D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05M CADMIUM SULFATE, 0.1M HEPES, REMARK 280 2.0M SODIUM ACETATE TRIHYDRATE, PH 7.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 287K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 88.45533 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 176.91067 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 132.68300 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 221.13833 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 44.22767 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 88.45533 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 176.91067 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 221.13833 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 132.68300 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 44.22767 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: 3650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -86.0 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 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 GLU A 64 REMARK 465 ALA A 65 REMARK 465 SER A 66 REMARK 465 GLU A 67 REMARK 465 ARG A 68 REMARK 465 TYR A 69 REMARK 465 PRO A 70 REMARK 465 GLU A 71 REMARK 465 ALA A 72 REMARK 465 LEU A 171 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 OE2 GLU A 91 NH2 ARG A 113 1.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 91 CD GLU A 91 OE2 0.105 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 3 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 15 NE - CZ - NH1 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 129 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 129 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP A 159 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES 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 NA A 207 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 14 O REMARK 620 2 HOH A 334 O 94.3 REMARK 620 3 HOH A 347 O 88.5 92.8 REMARK 620 4 HOH A 356 O 93.5 87.5 178.0 REMARK 620 5 HOH A 392 O 80.2 174.3 88.5 91.4 REMARK 620 6 HOH A 399 O 175.1 90.6 91.1 86.9 94.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 204 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 37 OE2 REMARK 620 2 GLU A 132 OE1 22.8 REMARK 620 3 HOH A 396 O 19.8 4.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 203 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 43 NE2 REMARK 620 2 GLU A 128 OE1 58.9 REMARK 620 3 GLU A 128 OE2 62.3 3.5 REMARK 620 4 GLU A 130 OE1 54.5 5.7 8.2 REMARK 620 5 GLU A 130 OE2 56.0 7.4 8.6 3.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 202 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 99 SG REMARK 620 2 HIS A 141 NE2 114.7 REMARK 620 3 HIS A 145 NE2 105.6 104.5 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 56T A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 207 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5CP0 RELATED DB: PDB REMARK 900 RELATED ID: 5CPD RELATED DB: PDB REMARK 900 RELATED ID: 5CVK RELATED DB: PDB REMARK 900 RELATED ID: 5CVP RELATED DB: PDB REMARK 900 RELATED ID: 5CVQ RELATED DB: PDB REMARK 900 RELATED ID: 5CWX RELATED DB: PDB REMARK 900 RELATED ID: 5CWY RELATED DB: PDB REMARK 900 RELATED ID: 5CX0 RELATED DB: PDB REMARK 900 RELATED ID: 5CY7 RELATED DB: PDB REMARK 900 RELATED ID: 5CY8 RELATED DB: PDB DBREF 5CXJ A 1 171 UNP Q5H3Z2 Q5H3Z2_XANOR 42 212 SEQRES 1 A 171 MET ILE ARG ASP ILE ILE ARG MET GLY ASP LYS ARG LEU SEQRES 2 A 171 LEU ARG VAL ALA PRO GLN VAL THR ASN LEU GLY SER ALA SEQRES 3 A 171 GLU LEU HIS ALA LEU VAL SER ASP MET PHE GLU THR MET SEQRES 4 A 171 GLY ALA ALA HIS GLY VAL GLY LEU ALA ALA PRO GLN ILE SEQRES 5 A 171 ALA VAL ASP LEU GLN LEU MET VAL PHE GLY PHE GLU ALA SEQRES 6 A 171 SER GLU ARG TYR PRO GLU ALA PRO ALA VAL PRO LEU THR SEQRES 7 A 171 ALA LEU ALA ASN ALA GLN ILE GLU PRO LEU SER ASP GLU SEQRES 8 A 171 MET GLU ASN GLY TRP GLU GLY CYS LEU SER ILE PRO GLY SEQRES 9 A 171 LEU ARG ALA VAL ILE PRO ARG TYR ARG TYR ILE ARG TYR SEQRES 10 A 171 ARG GLY PHE ALA PRO ASP GLY SER PRO ILE GLU ARG GLU SEQRES 11 A 171 ALA GLU GLY PHE HIS ALA ARG VAL VAL GLN HIS GLU TYR SEQRES 12 A 171 ASP HIS LEU VAL GLY ARG LEU TYR PRO SER ARG ILE GLU SEQRES 13 A 171 ASN PHE ASP THR PHE GLY PHE ASP ASP VAL LEU SER TYR SEQRES 14 A 171 ASP LEU HET ACT A 201 4 HET CD A 202 1 HET CD A 203 1 HET CD A 204 1 HET CD A 205 1 HET 56T A 206 16 HET NA A 207 1 HETNAM ACT ACETATE ION HETNAM CD CADMIUM ION HETNAM 56T 2-(FURAN-2-YL)ETHANAMINE HETNAM NA SODIUM ION FORMUL 2 ACT C2 H3 O2 1- FORMUL 3 CD 4(CD 2+) FORMUL 7 56T C6 H9 N O FORMUL 8 NA NA 1+ FORMUL 9 HOH *104(H2 O) HELIX 1 AA1 ASP A 10 LEU A 14 5 5 HELIX 2 AA2 SER A 25 ALA A 42 1 18 HELIX 3 AA3 PRO A 50 ALA A 53 5 4 HELIX 4 AA4 GLY A 133 VAL A 147 1 15 HELIX 5 AA5 LEU A 150 ILE A 155 5 6 HELIX 6 AA6 ASN A 157 PHE A 161 5 5 SHEET 1 AA1 5 GLY A 46 ALA A 48 0 SHEET 2 AA1 5 LEU A 58 PHE A 61 -1 O VAL A 60 N LEU A 47 SHEET 3 AA1 5 THR A 78 PRO A 87 -1 O THR A 78 N PHE A 61 SHEET 4 AA1 5 TYR A 114 PHE A 120 -1 O PHE A 120 N ALA A 81 SHEET 5 AA1 5 PRO A 126 GLU A 132 -1 O ILE A 127 N GLY A 119 SHEET 1 AA2 3 MET A 92 GLU A 97 0 SHEET 2 AA2 3 LEU A 105 TYR A 112 -1 O ALA A 107 N GLU A 97 SHEET 3 AA2 3 GLY A 162 PHE A 163 -1 O GLY A 162 N ARG A 106 LINK O LEU A 14 NA NA A 207 1555 1555 2.44 LINK OE2 GLU A 37 CD CD A 204 1555 8445 2.60 LINK NE2 HIS A 43 CD CD A 203 1555 8445 2.31 LINK SG CYS A 99 CD CD A 202 1555 1555 2.30 LINK OE1 GLU A 128 CD CD A 203 1555 1555 2.36 LINK OE2 GLU A 128 CD CD A 203 1555 1555 2.66 LINK OE1 GLU A 130 CD CD A 203 1555 1555 2.60 LINK OE2 GLU A 130 CD CD A 203 1555 1555 2.66 LINK OE1 GLU A 132 CD CD A 204 1555 1555 2.35 LINK NE2 HIS A 141 CD CD A 202 1555 1555 2.24 LINK OE2 GLU A 142 CD CD A 205 1555 1555 2.58 LINK NE2 HIS A 145 CD CD A 202 1555 1555 2.29 LINK CD CD A 204 O HOH A 396 1555 8545 2.59 LINK NA NA A 207 O HOH A 334 1555 8555 2.28 LINK NA NA A 207 O HOH A 347 1555 1555 2.40 LINK NA NA A 207 O HOH A 356 1555 8555 2.52 LINK NA NA A 207 O HOH A 392 1555 1555 2.81 LINK NA NA A 207 O HOH A 399 1555 8555 2.52 SITE 1 AC1 5 ARG A 149 LEU A 150 SER A 153 HOH A 309 SITE 2 AC1 5 HOH A 364 SITE 1 AC2 4 CYS A 99 HIS A 141 HIS A 145 CD A 205 SITE 1 AC3 3 HIS A 43 GLU A 128 GLU A 130 SITE 1 AC4 4 GLU A 37 GLU A 132 HOH A 395 HOH A 396 SITE 1 AC5 7 GLN A 51 HIS A 141 GLU A 142 HIS A 145 SITE 2 AC5 7 CD A 202 56T A 206 HOH A 366 SITE 1 AC6 11 HIS A 43 GLY A 44 VAL A 45 GLY A 46 SITE 2 AC6 11 GLU A 97 GLY A 98 CYS A 99 HIS A 141 SITE 3 AC6 11 GLU A 142 CD A 205 HOH A 381 SITE 1 AC7 6 LEU A 14 HOH A 334 HOH A 347 HOH A 356 SITE 2 AC7 6 HOH A 392 HOH A 399 CRYST1 58.702 58.702 265.366 90.00 90.00 120.00 P 61 2 2 12 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 0.017035 0.009835 0.000000 0.00000 SCALE2 0.000000 0.019671 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003768 0.00000