HEADER TRANSFERASE 28-MAY-16 5K8C TITLE X-RAY STRUCTURE OF KDNB, 3-DEOXY-ALPHA-D-MANNO-OCTULOSONATE 8-OXIDASE, TITLE 2 FROM SHEWANELLA ONEIDENSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-DEOXY-ALPHA-D-MANNO-OCTULOSONATE 8-OXIDASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.1.3.48; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SHEWANELLA ONEIDENSIS (STRAIN MR-1); SOURCE 3 ORGANISM_TAXID: 211586; SOURCE 4 STRAIN: MR-1; SOURCE 5 GENE: KDNB, SO_2477; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GROUP III ALCOHOL DEHYDROGENASE, 8-AMINO-3, 8-DIDEOXY-D-MANNO- KEYWDS 2 OCTULOSONIC ACID, DEOXY SUGAR, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.M.HOLDEN,J.B.THODEN,T.R.ZACHMAN-BROCKMEYER REVDAT 6 27-SEP-23 5K8C 1 REMARK REVDAT 5 25-DEC-19 5K8C 1 REMARK REVDAT 4 20-SEP-17 5K8C 1 JRNL REMARK REVDAT 3 24-AUG-16 5K8C 1 JRNL REVDAT 2 22-JUN-16 5K8C 1 JRNL REVDAT 1 15-JUN-16 5K8C 0 JRNL AUTH T.R.ZACHMAN-BROCKMEYER,J.B.THODEN,H.M.HOLDEN JRNL TITL STRUCTURES OF KDNB AND KDNA FROM SHEWANELLA ONEIDENSIS: KEY JRNL TITL 2 ENZYMES IN THE FORMATION OF JRNL TITL 3 8-AMINO-3,8-DIDEOXY-D-MANNO-OCTULOSONIC ACID. JRNL REF BIOCHEMISTRY V. 55 4485 2016 JRNL REFN ISSN 0006-2960 JRNL PMID 27275764 JRNL DOI 10.1021/ACS.BIOCHEM.6B00439 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0124 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 93.18 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 41818 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) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2218 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3021 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.82 REMARK 3 BIN R VALUE (WORKING SET) : 0.3180 REMARK 3 BIN FREE R VALUE SET COUNT : 149 REMARK 3 BIN FREE R VALUE : 0.3250 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2774 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 61 REMARK 3 SOLVENT ATOMS : 438 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.48000 REMARK 3 B22 (A**2) : 0.48000 REMARK 3 B33 (A**2) : -1.57000 REMARK 3 B12 (A**2) : 0.24000 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): 0.114 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.115 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.087 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.051 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2916 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2754 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3957 ; 2.042 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6367 ; 1.085 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 363 ; 6.559 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 122 ;36.577 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 500 ;14.761 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;21.318 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 438 ; 0.123 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3252 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 638 ; 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): 1437 ; 1.729 ; 1.650 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1436 ; 1.728 ; 1.650 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1796 ; 2.422 ; 2.467 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1797 ; 2.423 ; 2.468 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1479 ; 2.871 ; 1.964 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1479 ; 2.865 ; 1.964 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2159 ; 4.258 ; 2.830 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3768 ; 6.248 ;15.115 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3769 ; 6.247 ;15.120 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 : NULL 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 5K8C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1000221887. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER PLATINUM 135 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44036 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 93.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : 0.08300 REMARK 200 FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.39900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.100 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: PDB ENTRY 3RF7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 7-9% PEG-8000, 100 MM HOMOPIPES, 1 M REMARK 280 TETRAMETHYLAMMONIUM CHLORIDE, PH 5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 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 REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+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 -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 0.00000 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 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 74.93050 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 74.93050 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 74.93050 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 0.00000 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 0.00000 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 74.93050 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 74.93050 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 74.93050 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: 7950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -171.0 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 -0.500000 0.866025 0.000000 -161.39100 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 93.17914 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 299.72200 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 654 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 785 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 868 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 909 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 930 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 934 LIES ON A SPECIAL POSITION. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 MET A 1 CB CG SD CE 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 745 O HOH A 888 2.17 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 A 901 O HOH A 916 2775 2.08 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 MET A 12 CG - SD - CE ANGL. DEV. = -16.1 DEGREES REMARK 500 ASP A 23 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A 42 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ARG A 53 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 150 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 ASP A 181 CB - CG - OD1 ANGL. DEV. = 8.1 DEGREES REMARK 500 ASP A 181 CB - CG - OD2 ANGL. DEV. = -7.8 DEGREES REMARK 500 MET A 328 CG - SD - CE ANGL. DEV. = -10.0 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 HIS A 134 127.97 -38.44 REMARK 500 VAL A 158 -65.07 -99.79 REMARK 500 SER A 165 145.31 -172.97 REMARK 500 GLU A 229 -169.39 -120.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 VAL A 158 ARG A 159 -146.43 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 A 935 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A 936 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH A 937 DISTANCE = 6.41 ANGSTROMS REMARK 525 HOH A 938 DISTANCE = 6.69 ANGSTROMS 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 ZN A 407 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 194 OD1 REMARK 620 2 HIS A 258 NE2 97.8 REMARK 620 3 HIS A 272 NE2 99.2 107.6 REMARK 620 4 HOH A 807 O 157.8 93.7 95.3 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 NAD A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 407 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5K8B RELATED DB: BMCD DBREF 5K8C A 1 356 UNP Q8EEB0 KDNB_SHEON 1 356 SEQADV 5K8C GLY A -1 UNP Q8EEB0 EXPRESSION TAG SEQADV 5K8C HIS A 0 UNP Q8EEB0 EXPRESSION TAG SEQRES 1 A 358 GLY HIS MET SER PHE LYS ASN PHE LYS VAL VAL GLU LYS SEQRES 2 A 358 MET ILE PHE GLY ARG GLY SER PHE VAL GLN LEU ASP ASP SEQRES 3 A 358 VAL LEU ALA ALA GLN ARG LYS ALA ASP ASP ASP PHE VAL SEQRES 4 A 358 VAL PHE LEU VAL ASP ASP VAL HIS GLN GLY LYS PRO LEU SEQRES 5 A 358 GLU ALA ARG ILE PRO VAL LYS ALA GLN ASP LEU LEU ILE SEQRES 6 A 358 TRP VAL ASN VAL ASP GLU GLU PRO SER THR ILE GLN ILE SEQRES 7 A 358 ASP ALA LEU THR GLU GLN VAL GLN ALA PHE ASN GLY LYS SEQRES 8 A 358 LEU PRO VAL SER VAL VAL GLY LEU GLY GLY GLY SER THR SEQRES 9 A 358 MET ASP VAL ALA LYS ALA VAL SER LEU MET LEU THR ASN SEQRES 10 A 358 PRO GLY GLY SER ALA MET TYR GLN GLY TRP ASP LEU ILE SEQRES 11 A 358 LYS LYS PRO ALA VAL HIS HIS ILE GLY ILE PRO THR ILE SEQRES 12 A 358 SER GLY THR GLY ALA GLU ALA SER ARG THR ALA VAL LEU SEQRES 13 A 358 CYS GLY PRO VAL ARG LYS LEU GLY LEU ASN SER ASP TYR SEQRES 14 A 358 THR VAL PHE ASP GLN ILE ILE MET ASP SER GLU LEU ILE SEQRES 15 A 358 ASP GLY VAL GLU THR ASP GLN TRP PHE TYR THR GLY MET SEQRES 16 A 358 ASP CYS TYR ILE HIS CYS VAL GLU SER LEU GLU GLY THR SEQRES 17 A 358 PHE LEU ASN GLU PHE SER LYS ALA TYR ALA GLU LYS ALA SEQRES 18 A 358 MET ASP LEU CYS ARG GLN VAL TYR LEU GLU ASP HIS PRO SEQRES 19 A 358 GLU LYS ASP ASP LYS LEU MET MET ALA SER PHE MET GLY SEQRES 20 A 358 GLY MET SER ILE ALA TYR SER GLN VAL GLY ALA CYS HIS SEQRES 21 A 358 ALA VAL SER TYR GLY LEU SER TYR ILE LEU GLY TYR HIS SEQRES 22 A 358 HIS GLY ILE GLY ASN CYS ILE ALA PHE ASP VAL LEU GLU SEQRES 23 A 358 GLU PHE TYR PRO GLU GLY VAL ALA GLU PHE ARG LEU MET SEQRES 24 A 358 MET LYS LYS HIS ASN ILE THR LEU PRO LYS ASN ILE CYS SEQRES 25 A 358 LYS ASP LEU PRO ASP GLU THR ILE ALA LYS MET VAL ALA SEQRES 26 A 358 VAL THR LYS SER MET GLY PRO LEU TRP ALA ASN VAL TYR SEQRES 27 A 358 GLY PRO THR TRP GLU GLU LYS VAL THR ASP GLU MET LEU SEQRES 28 A 358 THR ALA LEU PHE ARG ARG ILE HET NAD A 401 44 HET PO4 A 402 5 HET PO4 A 403 5 HET CL A 404 1 HET EDO A 405 4 HET CL A 406 1 HET ZN A 407 1 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM PO4 PHOSPHATE ION HETNAM CL CHLORIDE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM ZN ZINC ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 NAD C21 H27 N7 O14 P2 FORMUL 3 PO4 2(O4 P 3-) FORMUL 5 CL 2(CL 1-) FORMUL 6 EDO C2 H6 O2 FORMUL 8 ZN ZN 2+ FORMUL 9 HOH *438(H2 O) HELIX 1 AA1 GLY A 17 VAL A 20 5 4 HELIX 2 AA2 GLN A 21 ARG A 30 1 10 HELIX 3 AA3 VAL A 44 GLN A 46 5 3 HELIX 4 AA4 LYS A 48 ILE A 54 1 7 HELIX 5 AA5 SER A 72 ASN A 87 1 16 HELIX 6 AA6 GLY A 99 LEU A 113 1 15 HELIX 7 AA7 SER A 119 GLN A 123 5 5 HELIX 8 AA8 SER A 165 VAL A 169 5 5 HELIX 9 AA9 ASP A 176 ASP A 181 5 6 HELIX 10 AB1 GLU A 184 GLU A 204 1 21 HELIX 11 AB2 ASN A 209 GLU A 229 1 21 HELIX 12 AB3 GLU A 233 SER A 248 1 16 HELIX 13 AB4 ILE A 249 SER A 252 5 4 HELIX 14 AB5 GLY A 255 GLY A 269 1 15 HELIX 15 AB6 HIS A 271 ASP A 281 1 11 HELIX 16 AB7 TYR A 287 HIS A 301 1 15 HELIX 17 AB8 PRO A 314 SER A 327 1 14 HELIX 18 AB9 MET A 328 GLY A 337 1 10 HELIX 19 AC1 THR A 339 LYS A 343 5 5 HELIX 20 AC2 THR A 345 ILE A 356 1 12 SHEET 1 AA1 6 LYS A 11 PHE A 14 0 SHEET 2 AA1 6 GLN A 172 MET A 175 1 O MET A 175 N ILE A 13 SHEET 3 AA1 6 HIS A 135 PRO A 139 1 N GLY A 137 O GLN A 172 SHEET 4 AA1 6 SER A 93 GLY A 98 1 N GLY A 96 O ILE A 136 SHEET 5 AA1 6 VAL A 37 ASP A 42 1 N VAL A 38 O VAL A 95 SHEET 6 AA1 6 LEU A 61 VAL A 65 1 O VAL A 65 N VAL A 41 SHEET 1 AA2 3 GLY A 124 TRP A 125 0 SHEET 2 AA2 3 LYS A 160 ASN A 164 1 O GLY A 162 N GLY A 124 SHEET 3 AA2 3 VAL A 153 CYS A 155 -1 N LEU A 154 O LEU A 161 LINK OD1 ASP A 194 ZN ZN A 407 1555 1555 2.24 LINK NE2 HIS A 258 ZN ZN A 407 1555 1555 2.40 LINK NE2 HIS A 272 ZN ZN A 407 1555 1555 2.16 LINK ZN ZN A 407 O HOH A 807 1555 1555 2.44 SITE 1 AC1 37 ASP A 42 VAL A 44 HIS A 45 VAL A 67 SITE 2 AC1 37 GLU A 70 PRO A 71 GLY A 99 GLY A 100 SITE 3 AC1 37 SER A 101 ASP A 104 THR A 140 ILE A 141 SITE 4 AC1 37 THR A 144 ALA A 146 SER A 149 THR A 151 SITE 5 AC1 37 VAL A 153 LYS A 160 LEU A 179 VAL A 183 SITE 6 AC1 37 GLN A 187 THR A 191 ASP A 194 HOH A 520 SITE 7 AC1 37 HOH A 544 HOH A 561 HOH A 617 HOH A 629 SITE 8 AC1 37 HOH A 632 HOH A 658 HOH A 663 HOH A 692 SITE 9 AC1 37 HOH A 697 HOH A 707 HOH A 709 HOH A 749 SITE 10 AC1 37 HOH A 751 SITE 1 AC2 6 ASP A 34 ASP A 181 VAL A 183 TRP A 188 SITE 2 AC2 6 ASP A 235 EDO A 405 SITE 1 AC3 9 GLU A 204 PHE A 286 TYR A 287 PRO A 288 SITE 2 AC3 9 GLU A 289 GLY A 290 HOH A 505 HOH A 527 SITE 3 AC3 9 HOH A 766 SITE 1 AC4 4 HIS A 271 ILE A 274 HOH A 911 HOH A 931 SITE 1 AC5 5 THR A 185 HIS A 301 PO4 A 402 HOH A 509 SITE 2 AC5 5 HOH A 712 SITE 1 AC6 2 GLN A 75 HOH A 660 SITE 1 AC7 6 ASP A 194 HIS A 258 HIS A 272 ASN A 276 SITE 2 AC7 6 HOH A 773 HOH A 807 CRYST1 107.594 107.594 149.861 90.00 90.00 120.00 P 63 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 0.009294 0.005366 0.000000 0.00000 SCALE2 0.000000 0.010732 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006673 0.00000