HEADER HYDROLASE 02-DEC-13 4NT8 TITLE FORMYL-METHIONINE-ALANINE COMPLEX STRUCTURE OF PEPTIDE DEFORMYLASE TITLE 2 FROM XANTHOMOONAS ORYZAE PV. ORYZAE 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; SOURCE 3 ORGANISM_TAXID: 291331; SOURCE 4 STRAIN: KACC10331 / KXO85; SOURCE 5 GENE: DEF, XOO1075; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS METALLOPEPTIDASE, PEPTIDE DEFORMYLASE, CADMIUM, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.P.T.NGO,J.K.KIM,L.W.KANG REVDAT 2 08-NOV-23 4NT8 1 REMARK LINK REVDAT 1 03-DEC-14 4NT8 0 JRNL AUTH H.P.T.NGO,J.K.KIM,L.W.KANG JRNL TITL SUBSTRATE COMPLEX STRUCTURE OF XOO1075, A PEPTIDE JRNL TITL 2 DEFORMYLASE, FROM XANTHOMONAS ORYZAE PV. ORYZAE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 6.4.0 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.35 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 13852 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) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 729 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1005 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.72 REMARK 3 BIN R VALUE (WORKING SET) : 0.2850 REMARK 3 BIN FREE R VALUE SET COUNT : 50 REMARK 3 BIN FREE R VALUE : 0.2980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1317 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 96 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : 0.02000 REMARK 3 B33 (A**2) : -0.05000 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): 0.181 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.171 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.140 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.790 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1395 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1298 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1855 ; 1.856 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2973 ; 0.923 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 168 ; 7.014 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 67 ;33.067 ;22.836 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 212 ;15.661 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;18.900 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 200 ; 0.112 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1563 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 322 ; 0.001 ; 0.020 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): 678 ; 1.913 ; 2.745 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 677 ; 1.894 ; 2.741 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 844 ; 2.877 ; 4.097 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 848 ; 3.128 ; 4.177 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 716 ; 3.252 ; 3.154 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 699 ; 3.115 ; 3.228 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1022 ; 4.884 ; 4.706 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1591 ; 6.967 ;23.267 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1592 ; 6.967 ;23.295 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 ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4NT8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-DEC-13. REMARK 100 THE DEPOSITION ID IS D_1000083626. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-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) : 0.99999 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 : 16778 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 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 : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: 4FR8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05M CADMIUM SULFATE, 0.1M HEPES PH REMARK 280 7.5, 2.0M SODIUM ACETATE TRIHYDRATE, 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 88.72933 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 177.45867 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 133.09400 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 221.82333 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 44.36467 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 88.72933 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 177.45867 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 221.82333 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 133.09400 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 44.36467 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: 3750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15110 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 384 LIES ON A SPECIAL POSITION. 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 TYR A 169 REMARK 465 ASP A 170 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 O HOH A 366 O HOH A 372 1.86 REMARK 500 O HOH A 302 O HOH A 360 2.03 REMARK 500 OE2 GLU A 130 O HOH A 373 2.11 REMARK 500 OH TYR A 69 OXT ALA A 208 2.17 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 116 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG A 116 NE - CZ - NH2 ANGL. DEV. = -4.5 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 CD A 201 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 37 OE2 REMARK 620 2 HOH A 366 O 147.6 REMARK 620 3 HOH A 367 O 91.8 107.5 REMARK 620 4 HOH A 372 O 102.2 49.8 151.3 REMARK 620 N 1 2 3 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 CSD A 99 OD2 REMARK 620 2 CSD A 99 SG 30.4 REMARK 620 3 HIS A 141 NE2 83.6 107.2 REMARK 620 4 HIS A 145 NE2 80.7 93.2 104.6 REMARK 620 5 FME A 207 O1 171.3 155.8 94.5 91.6 REMARK 620 6 HOH A 362 O 116.7 90.3 110.0 142.5 71.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 206 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 105 O REMARK 620 2 ASP A 164 OD2 121.5 REMARK 620 3 HOH A 337 O 93.9 125.4 REMARK 620 4 HOH A 359 O 108.7 79.6 129.9 REMARK 620 N 1 2 3 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 GLU A 128 OE1 REMARK 620 2 GLU A 128 OE2 56.8 REMARK 620 3 GLU A 130 OE2 124.6 139.8 REMARK 620 4 GLU A 130 OE1 86.1 142.7 57.0 REMARK 620 5 HOH A 368 O 102.3 72.2 68.5 117.0 REMARK 620 6 HOH A 373 O 168.6 113.5 57.7 102.9 67.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 205 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 148 O REMARK 620 2 HOH A 370 O 86.2 REMARK 620 3 HOH A 371 O 112.4 58.7 REMARK 620 4 HOH A 374 O 130.1 62.0 84.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD 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 ACT A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FME A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ALA A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 209 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DLD RELATED DB: PDB REMARK 900 NATIVE STRUCTURE DBREF 4NT8 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 CSD 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 MODRES 4NT8 CSD A 99 CYS 3-SULFINOALANINE HET CSD A 99 8 HET CD A 201 1 HET CD A 202 1 HET CD A 203 1 HET ACT A 204 4 HET NA A 205 1 HET NA A 206 1 HET FME A 207 10 HET ALA A 208 6 HET GOL A 209 6 HETNAM CSD 3-SULFINOALANINE HETNAM CD CADMIUM ION HETNAM ACT ACETATE ION HETNAM NA SODIUM ION HETNAM FME N-FORMYLMETHIONINE HETNAM ALA ALANINE HETNAM GOL GLYCEROL HETSYN CSD S-CYSTEINESULFINIC ACID; S-SULFINOCYSTEINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 CSD C3 H7 N O4 S FORMUL 2 CD 3(CD 2+) FORMUL 5 ACT C2 H3 O2 1- FORMUL 6 NA 2(NA 1+) FORMUL 8 FME C6 H11 N O3 S FORMUL 9 ALA C3 H7 N O2 FORMUL 10 GOL C3 H8 O3 FORMUL 11 HOH *96(H2 O) HELIX 1 1 ASP A 10 ARG A 15 5 6 HELIX 2 2 SER A 25 ALA A 42 1 18 HELIX 3 3 PRO A 50 ALA A 53 5 4 HELIX 4 4 GLY A 133 VAL A 147 1 15 HELIX 5 5 LEU A 150 ILE A 155 5 6 HELIX 6 6 ASN A 157 PHE A 161 5 5 SHEET 1 A 5 GLY A 46 ALA A 48 0 SHEET 2 A 5 LEU A 58 PHE A 63 -1 O VAL A 60 N LEU A 47 SHEET 3 A 5 VAL A 75 PRO A 87 -1 O THR A 78 N PHE A 61 SHEET 4 A 5 TYR A 114 PHE A 120 -1 O PHE A 120 N ALA A 81 SHEET 5 A 5 PRO A 126 GLU A 132 -1 O ILE A 127 N GLY A 119 SHEET 1 B 3 MET A 92 CSD A 99 0 SHEET 2 B 3 ILE A 102 TYR A 112 -1 O ILE A 109 N GLY A 95 SHEET 3 B 3 GLY A 162 PHE A 163 -1 O GLY A 162 N ARG A 106 LINK C GLY A 98 N CSD A 99 1555 1555 1.33 LINK C CSD A 99 N LEU A 100 1555 1555 1.32 LINK C FME A 207 N ALA A 208 1555 1555 1.32 LINK OE2 GLU A 37 CD CD A 201 1555 1555 2.21 LINK OD2 CSD A 99 CD CD A 202 1555 1555 2.12 LINK SG CSD A 99 CD CD A 202 1555 1555 2.77 LINK O LEU A 105 NA NA A 206 1555 1555 2.34 LINK OE1 GLU A 128 CD CD A 203 1555 1555 2.23 LINK OE2 GLU A 128 CD CD A 203 1555 1555 2.24 LINK OE2 GLU A 130 CD CD A 203 1555 1555 2.20 LINK OE1 GLU A 130 CD CD A 203 1555 1555 2.29 LINK NE2 HIS A 141 CD CD A 202 1555 1555 2.26 LINK NE2 HIS A 145 CD CD A 202 1555 1555 2.23 LINK O GLY A 148 NA NA A 205 1555 1555 2.34 LINK OD2 ASP A 164 NA NA A 206 1555 1555 2.28 LINK CD CD A 201 O HOH A 366 1555 1555 2.21 LINK CD CD A 201 O HOH A 367 1555 1555 2.23 LINK CD CD A 201 O HOH A 372 1555 1555 2.20 LINK CD CD A 202 O1 FME A 207 1555 1555 2.21 LINK CD CD A 202 O HOH A 362 1555 1555 2.33 LINK CD CD A 203 O HOH A 368 1555 1555 2.23 LINK CD CD A 203 O HOH A 373 1555 1555 2.18 LINK NA NA A 205 O HOH A 370 1555 1555 2.30 LINK NA NA A 205 O HOH A 371 1555 1555 2.25 LINK NA NA A 205 O HOH A 374 1555 1555 2.22 LINK NA NA A 206 O HOH A 337 1555 1555 2.26 LINK NA NA A 206 O HOH A 359 1555 1555 2.26 SITE 1 AC1 5 GLU A 37 GLU A 132 HOH A 366 HOH A 367 SITE 2 AC1 5 HOH A 372 SITE 1 AC2 6 GLN A 51 CSD A 99 HIS A 141 HIS A 145 SITE 2 AC2 6 FME A 207 HOH A 362 SITE 1 AC3 5 HIS A 43 GLU A 128 GLU A 130 HOH A 368 SITE 2 AC3 5 HOH A 373 SITE 1 AC4 8 LEU A 14 ARG A 149 LEU A 150 SER A 153 SITE 2 AC4 8 ASP A 159 HOH A 350 HOH A 378 HOH A 385 SITE 1 AC5 6 LEU A 14 GLY A 148 ASP A 159 HOH A 370 SITE 2 AC5 6 HOH A 371 HOH A 374 SITE 1 AC6 4 LEU A 105 ASP A 164 HOH A 337 HOH A 359 SITE 1 AC7 12 GLY A 44 VAL A 45 GLY A 46 GLN A 51 SITE 2 AC7 12 GLY A 98 PHE A 134 HIS A 141 GLU A 142 SITE 3 AC7 12 HIS A 145 CD A 202 ALA A 208 HOH A 362 SITE 1 AC8 5 ARG A 68 TYR A 69 GLY A 98 LEU A 100 SITE 2 AC8 5 FME A 207 SITE 1 AC9 2 ASN A 22 HOH A 394 CRYST1 58.584 58.584 266.188 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 0.017070 0.009855 0.000000 0.00000 SCALE2 0.000000 0.019710 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003757 0.00000