HEADER ISOMERASE 06-MAY-19 6K0G TITLE CRYSTAL STRUCTURE OF UDP-GLUCOSE 4-EPIMERASE FROM BIFIDOBACTERIUM TITLE 2 LONGUM IN COMPLEX WITH NAD+ AND UDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: UDP-GLUCOSE 4-EPIMERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UDP-GALACTOSE 4-EPIMERASE; COMPND 5 EC: 5.1.3.2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BIFIDOBACTERIUM LONGUM SUBSP. LONGUM (STRAIN SOURCE 3 ATCC 15707 / DSM 20219 / JCM 1217 / NCTC 11818 / E194B); SOURCE 4 ORGANISM_TAXID: 565042; SOURCE 5 STRAIN: ATCC 15707 / DSM 20219 / JCM 1217 / NCTC 11818 / E194B; SOURCE 6 VARIANT: JCM 1217; SOURCE 7 GENE: LNPD, BLLJ_1620; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_VARIANT: CODONPLUS (DE3)-RIL; SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PET-30 KEYWDS ROSSMANN FOLD, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.-W.NAM,M.NISHIMOTO,T.ARAKAWA,M.KITAOKA,S.FUSHINOBU REVDAT 3 22-NOV-23 6K0G 1 REMARK REVDAT 2 14-AUG-19 6K0G 1 JRNL REVDAT 1 07-AUG-19 6K0G 0 JRNL AUTH Y.W.NAM,M.NISHIMOTO,T.ARAKAWA,M.KITAOKA,S.FUSHINOBU JRNL TITL STRUCTURAL BASIS FOR BROAD SUBSTRATE SPECIFICITY OF JRNL TITL 2 UDP-GLUCOSE 4-EPIMERASE IN THE HUMAN MILK OLIGOSACCHARIDE JRNL TITL 3 CATABOLIC PATHWAY OF BIFIDOBACTERIUM LONGUM. JRNL REF SCI REP V. 9 11081 2019 JRNL REFN ESSN 2045-2322 JRNL PMID 31366978 JRNL DOI 10.1038/S41598-019-47591-W REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0222 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 42417 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) : 0.151 REMARK 3 R VALUE (WORKING SET) : 0.149 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2250 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2994 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.1620 REMARK 3 BIN FREE R VALUE SET COUNT : 165 REMARK 3 BIN FREE R VALUE : 0.2240 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2588 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 70 REMARK 3 SOLVENT ATOMS : 375 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.33 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) : 0.01000 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): 0.086 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.088 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.053 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.697 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2723 ; 0.014 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): 2447 ; 0.002 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3721 ; 1.725 ; 1.694 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5721 ; 1.089 ; 1.659 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 334 ; 6.781 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 123 ;34.646 ;23.821 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 428 ;11.558 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;12.965 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 360 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3011 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 498 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 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 : 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6K0G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1300012066. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAY-13 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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NUMERICAL LINK TYPE SI(111) REMARK 200 DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44804 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 18.10 REMARK 200 R MERGE (I) : 0.12200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 20.60 REMARK 200 R MERGE FOR SHELL (I) : 0.57300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1EK6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% (V/V) PEG 400, 0.2 M MGCL, 0.1 M REMARK 280 HEPES-NAOH (PH 7.5), 10 MM UDP, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 213.71867 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 106.85933 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 160.28900 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 53.42967 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 267.14833 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 213.71867 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 106.85933 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 53.42967 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 160.28900 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 267.14833 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: 6010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 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 MET A 1 REMARK 465 ARG A 337 REMARK 465 ASP A 338 REMARK 465 ALA A 339 REMARK 465 GLU A 340 REMARK 465 LEU A 341 REMARK 465 GLU A 342 REMARK 465 HIS A 343 REMARK 465 HIS A 344 REMARK 465 HIS A 345 REMARK 465 HIS A 346 REMARK 465 HIS A 347 REMARK 465 HIS A 348 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 315 CD GLU A 315 OE2 -0.067 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 PHE A 179 CB - CA - C ANGL. DEV. = 12.1 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 ASN A 36 29.62 -140.05 REMARK 500 ASP A 168 85.24 -152.97 REMARK 500 PHE A 179 -113.00 -87.62 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 MG A 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 67 OE2 REMARK 620 2 HOH A 809 O 150.0 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UDP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 403 DBREF 6K0G A 1 340 UNP E8MF10 GALE_BIFL2 1 340 SEQADV 6K0G LEU A 341 UNP E8MF10 EXPRESSION TAG SEQADV 6K0G GLU A 342 UNP E8MF10 EXPRESSION TAG SEQADV 6K0G HIS A 343 UNP E8MF10 EXPRESSION TAG SEQADV 6K0G HIS A 344 UNP E8MF10 EXPRESSION TAG SEQADV 6K0G HIS A 345 UNP E8MF10 EXPRESSION TAG SEQADV 6K0G HIS A 346 UNP E8MF10 EXPRESSION TAG SEQADV 6K0G HIS A 347 UNP E8MF10 EXPRESSION TAG SEQADV 6K0G HIS A 348 UNP E8MF10 EXPRESSION TAG SEQRES 1 A 348 MET THR THR VAL LEU VAL THR GLY GLY ALA GLY PHE ILE SEQRES 2 A 348 ALA THR HIS THR ASP ILE GLU LEU LEU ASN LYS GLY TYR SEQRES 3 A 348 ASP VAL ILE SER VAL ASP ASN TYR GLY ASN SER SER PRO SEQRES 4 A 348 VAL ALA LEU GLU ARG VAL GLU GLN ILE THR GLY LYS PRO SEQRES 5 A 348 VAL LYS ARG TYR ASP GLY ASP VAL ARG ASP GLU ALA LEU SEQRES 6 A 348 MET GLU ARG VAL PHE ALA GLU ASN ASN ILE ASP TRP VAL SEQRES 7 A 348 ILE HIS PHE ALA GLY LEU LYS ALA VAL GLY GLU SER VAL SEQRES 8 A 348 ALA LYS PRO ILE GLU TYR TYR ASP ASN ASN LEU TYR SER SEQRES 9 A 348 THR LEU VAL LEU LEU LYS VAL MET LYS LYS HIS ASN VAL SEQRES 10 A 348 LYS LYS ILE ILE PHE SER SER SER ALA THR VAL TYR GLY SEQRES 11 A 348 THR PRO LYS GLU LEU PRO ILE THR GLU GLU THR PRO THR SEQRES 12 A 348 GLY GLY THR THR ASN PRO TYR GLY THR SER LYS LEU PHE SEQRES 13 A 348 GLN GLU GLN ILE LEU ARG ASP VAL HIS VAL ALA ASP PRO SEQRES 14 A 348 SER TRP THR ILE VAL LEU LEU ARG TYR PHE ASN PRO VAL SEQRES 15 A 348 GLY ALA HIS GLU SER GLY LEU LEU GLY GLU ASP PRO LYS SEQRES 16 A 348 GLY ILE PRO ALA ASN LEU THR PRO TYR VAL ALA LYS VAL SEQRES 17 A 348 ALA VAL GLY GLU LEU LYS GLU VAL GLN VAL TYR GLY ASP SEQRES 18 A 348 ASP TYR ASP THR PRO ASP GLY THR GLY VAL ARG ASP TYR SEQRES 19 A 348 ILE HIS VAL VAL ASP LEU ALA LYS GLY HIS VAL ALA VAL SEQRES 20 A 348 ILE ASP HIS ILE ASP LYS GLU GLY VAL PHE VAL TYR ASN SEQRES 21 A 348 LEU GLY THR GLY HIS GLY TYR SER VAL LEU GLU VAL ILE SEQRES 22 A 348 LYS ALA TYR GLU LYS ALA ALA GLY HIS PRO ILE PRO TYR SEQRES 23 A 348 ALA ILE LYS PRO ARG ARG PRO GLY ASP ILE ALA ALA CYS SEQRES 24 A 348 TYR ALA ASP ALA SER LYS ALA GLU LYS GLU LEU GLY TRP SEQRES 25 A 348 LYS ALA GLU LEU THR ILE ASP ASP MET ALA ALA SER SER SEQRES 26 A 348 LEU ASN TRP GLN THR LYS ASN PRO ASN GLY PHE ARG ASP SEQRES 27 A 348 ALA GLU LEU GLU HIS HIS HIS HIS HIS HIS HET UDP A 401 25 HET NAD A 402 44 HET MG A 403 1 HETNAM UDP URIDINE-5'-DIPHOSPHATE HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM MG MAGNESIUM ION FORMUL 2 UDP C9 H14 N2 O12 P2 FORMUL 3 NAD C21 H27 N7 O14 P2 FORMUL 4 MG MG 2+ FORMUL 5 HOH *375(H2 O) HELIX 1 AA1 GLY A 11 LYS A 24 1 14 HELIX 2 AA2 PRO A 39 GLY A 50 1 12 HELIX 3 AA3 ASP A 62 ASN A 73 1 12 HELIX 4 AA4 ALA A 86 LYS A 93 1 8 HELIX 5 AA5 LYS A 93 HIS A 115 1 23 HELIX 6 AA6 THR A 127 GLY A 130 5 4 HELIX 7 AA7 ASN A 148 ASP A 168 1 21 HELIX 8 AA8 ASN A 200 VAL A 210 1 11 HELIX 9 AA9 VAL A 237 ILE A 251 1 15 HELIX 10 AB1 VAL A 269 GLY A 281 1 13 HELIX 11 AB2 ALA A 303 GLY A 311 1 9 HELIX 12 AB3 THR A 317 ASN A 332 1 16 SHEET 1 AA1 7 LYS A 54 ASP A 57 0 SHEET 2 AA1 7 ASP A 27 ASP A 32 1 N SER A 30 O LYS A 54 SHEET 3 AA1 7 THR A 3 THR A 7 1 N VAL A 6 O ILE A 29 SHEET 4 AA1 7 TRP A 77 HIS A 80 1 O ILE A 79 N LEU A 5 SHEET 5 AA1 7 LYS A 119 SER A 125 1 O ILE A 121 N HIS A 80 SHEET 6 AA1 7 THR A 172 TYR A 178 1 O VAL A 174 N PHE A 122 SHEET 7 AA1 7 GLY A 255 LEU A 261 1 O TYR A 259 N ARG A 177 SHEET 1 AA2 3 ASN A 180 VAL A 182 0 SHEET 2 AA2 3 VAL A 231 HIS A 236 1 O ASP A 233 N ASN A 180 SHEET 3 AA2 3 GLY A 266 SER A 268 -1 O TYR A 267 N ARG A 232 SHEET 1 AA3 3 ASN A 180 VAL A 182 0 SHEET 2 AA3 3 VAL A 231 HIS A 236 1 O ASP A 233 N ASN A 180 SHEET 3 AA3 3 ALA A 298 CYS A 299 1 O CYS A 299 N VAL A 231 SHEET 1 AA4 2 VAL A 216 TYR A 219 0 SHEET 2 AA4 2 TYR A 286 LYS A 289 1 O LYS A 289 N VAL A 218 LINK OE2 GLU A 67 MG MG A 403 1555 1555 2.27 LINK MG MG A 403 O HOH A 809 1555 1555 2.49 CISPEP 1 LEU A 135 PRO A 136 0 -4.42 SITE 1 AC1 22 ASN A 180 ALA A 199 ASN A 200 LEU A 201 SITE 2 AC1 22 GLN A 217 VAL A 218 TYR A 219 GLY A 230 SITE 3 AC1 22 ARG A 232 TYR A 234 VAL A 269 ARG A 292 SITE 4 AC1 22 ASP A 295 HOH A 513 HOH A 529 HOH A 551 SITE 5 AC1 22 HOH A 610 HOH A 659 HOH A 661 HOH A 670 SITE 6 AC1 22 HOH A 715 HOH A 721 SITE 1 AC2 34 GLY A 8 GLY A 11 PHE A 12 ILE A 13 SITE 2 AC2 34 ASP A 32 ASN A 33 TYR A 34 GLY A 35 SITE 3 AC2 34 ASN A 36 SER A 37 GLY A 58 ASP A 59 SITE 4 AC2 34 VAL A 60 PHE A 81 ALA A 82 GLY A 83 SITE 5 AC2 34 LYS A 85 ASN A 100 SER A 123 SER A 124 SITE 6 AC2 34 TYR A 150 LYS A 154 TYR A 178 PHE A 179 SITE 7 AC2 34 PRO A 181 HOH A 529 HOH A 550 HOH A 560 SITE 8 AC2 34 HOH A 575 HOH A 615 HOH A 620 HOH A 636 SITE 9 AC2 34 HOH A 695 HOH A 724 SITE 1 AC3 3 GLU A 67 HIS A 115 HOH A 809 CRYST1 70.235 70.235 320.578 90.00 90.00 120.00 P 65 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 0.014238 0.008220 0.000000 0.00000 SCALE2 0.000000 0.016441 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003119 0.00000