HEADER ISOMERASE 06-MAY-19 6K0H TITLE CRYSTAL STRUCTURE OF UDP-GLUCOSE 4-EPIMERASE FROM BIFIDOBACTERIUM TITLE 2 LONGUM IN COMPLEX WITH NAD+ AND UDP-GLCNAC 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: GALE, 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, HYDROLASE, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.-W.NAM,M.NISHIMOTO,T.ARAKAWA,M.KITAOKA,S.FUSHINOBU REVDAT 3 22-NOV-23 6K0H 1 LINK REVDAT 2 14-AUG-19 6K0H 1 JRNL REVDAT 1 07-AUG-19 6K0H 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. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0230 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 30845 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 : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1649 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2212 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.64 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE SET COUNT : 115 REMARK 3 BIN FREE R VALUE : 0.2800 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 : 99 REMARK 3 SOLVENT ATOMS : 211 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.79 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): 0.143 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.138 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2750 ; 0.012 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): 2476 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3753 ; 1.661 ; 1.705 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5791 ; 1.492 ; 1.675 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 334 ; 7.030 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 123 ;34.649 ;23.821 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 428 ;13.619 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;12.597 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 365 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3018 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 500 ; 0.011 ; 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 6K0H 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_1300012067. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-14 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-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 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 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32699 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 : 16.90 REMARK 200 R MERGE (I) : 0.12400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 17.00 REMARK 200 R MERGE FOR SHELL (I) : 0.95100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.500 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 (%): 59.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% (V/V) PEG400, 0.2 M MGCL, 0.1 M REMARK 280 HEPES-NAOH (PH 7.5), AND 10 MM UDP-GLCNAC, VAPOR DIFFUSION, REMARK 280 SITTING DROP, 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 214.65733 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 107.32867 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 160.99300 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 53.66433 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 268.32167 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 214.65733 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 107.32867 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 53.66433 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 160.99300 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 268.32167 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: 7500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 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 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. = 14.9 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 ASP A 168 85.35 -156.15 REMARK 500 PHE A 179 -130.08 -84.66 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 ALA A 301 ASP A 302 149.24 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 405 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 46 OE1 REMARK 620 2 GLU A 46 OE2 52.7 REMARK 620 3 LYS A 308 O 55.8 5.8 REMARK 620 4 HOH A 639 O 51.7 10.9 7.4 REMARK 620 5 HOH A 683 O 54.7 9.8 5.0 3.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 406 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 266 O REMARK 620 2 HOH A 525 O 74.9 REMARK 620 3 HOH A 661 O 89.8 164.6 REMARK 620 4 HOH A 663 O 76.3 75.8 98.5 REMARK 620 5 HOH A 690 O 89.8 69.1 114.1 144.6 REMARK 620 6 HOH A 710 O 170.7 96.7 98.4 98.0 90.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UD1 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 406 DBREF 6K0H A 1 340 UNP E8MF10 GALE_BIFL2 1 340 SEQADV 6K0H LEU A 341 UNP E8MF10 EXPRESSION TAG SEQADV 6K0H GLU A 342 UNP E8MF10 EXPRESSION TAG SEQADV 6K0H HIS A 343 UNP E8MF10 EXPRESSION TAG SEQADV 6K0H HIS A 344 UNP E8MF10 EXPRESSION TAG SEQADV 6K0H HIS A 345 UNP E8MF10 EXPRESSION TAG SEQADV 6K0H HIS A 346 UNP E8MF10 EXPRESSION TAG SEQADV 6K0H HIS A 347 UNP E8MF10 EXPRESSION TAG SEQADV 6K0H 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 PEG A 401 7 HET PEG A 402 7 HET NAD A 403 44 HET UD1 A 404 39 HET MG A 405 1 HET MG A 406 1 HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM UD1 URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE HETNAM MG MAGNESIUM ION FORMUL 2 PEG 2(C4 H10 O3) FORMUL 4 NAD C21 H27 N7 O14 P2 FORMUL 5 UD1 C17 H27 N3 O17 P2 FORMUL 6 MG 2(MG 2+) FORMUL 8 HOH *211(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 VAL A 53 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 PHE A 257 N ILE A 173 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 2 VAL A 216 TYR A 219 0 SHEET 2 AA3 2 TYR A 286 LYS A 289 1 O LYS A 289 N VAL A 218 LINK OE1 GLU A 46 MG MG A 405 1555 8665 2.33 LINK OE2 GLU A 46 MG MG A 405 1555 8665 2.51 LINK O GLY A 266 MG MG A 406 1555 1555 2.33 LINK O LYS A 308 MG MG A 405 1555 1555 2.48 LINK MG MG A 405 O HOH A 639 1555 8565 2.79 LINK MG MG A 405 O HOH A 683 1555 1555 2.23 LINK MG MG A 406 O HOH A 525 1555 1555 2.54 LINK MG MG A 406 O HOH A 661 1555 1555 2.65 LINK MG MG A 406 O HOH A 663 1555 1555 2.54 LINK MG MG A 406 O HOH A 690 1555 1555 2.41 LINK MG MG A 406 O HOH A 710 1555 1555 2.30 CISPEP 1 LEU A 135 PRO A 136 0 -1.72 SITE 1 AC1 5 ILE A 273 LYS A 274 GLU A 277 TYR A 286 SITE 2 AC1 5 HOH A 508 SITE 1 AC2 3 LYS A 253 TYR A 259 GLU A 309 SITE 1 AC3 33 GLY A 8 GLY A 11 PHE A 12 ILE A 13 SITE 2 AC3 33 ASP A 32 ASN A 33 TYR A 34 GLY A 35 SITE 3 AC3 33 ASN A 36 SER A 37 GLY A 58 ASP A 59 SITE 4 AC3 33 VAL A 60 PHE A 81 ALA A 82 GLY A 83 SITE 5 AC3 33 LYS A 85 ASN A 100 SER A 124 TYR A 150 SITE 6 AC3 33 LYS A 154 TYR A 178 PHE A 179 PRO A 181 SITE 7 AC3 33 UD1 A 404 HOH A 520 HOH A 554 HOH A 561 SITE 8 AC3 33 HOH A 571 HOH A 618 HOH A 620 HOH A 625 SITE 9 AC3 33 HOH A 626 SITE 1 AC4 27 LYS A 85 SER A 125 TYR A 150 TYR A 178 SITE 2 AC4 27 PHE A 179 ASN A 180 ALA A 199 ASN A 200 SITE 3 AC4 27 LEU A 201 GLN A 217 VAL A 218 TYR A 219 SITE 4 AC4 27 GLY A 230 ARG A 232 TYR A 234 VAL A 269 SITE 5 AC4 27 ARG A 292 ASP A 295 NAD A 403 HOH A 501 SITE 6 AC4 27 HOH A 529 HOH A 582 HOH A 585 HOH A 597 SITE 7 AC4 27 HOH A 609 HOH A 646 HOH A 655 SITE 1 AC5 4 GLU A 46 LYS A 308 HOH A 639 HOH A 683 SITE 1 AC6 6 GLY A 266 HOH A 525 HOH A 661 HOH A 663 SITE 2 AC6 6 HOH A 690 HOH A 710 CRYST1 69.450 69.450 321.986 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 0.014399 0.008313 0.000000 0.00000 SCALE2 0.000000 0.016626 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003106 0.00000