HEADER ISOMERASE 12-AUG-09 3INR TITLE STRUCTURE OF UDP-GALACTOPYRANOSE MUTASE BOUND TO UDP-GALACTOSE TITLE 2 (OXIDIZED) COMPND MOL_ID: 1; COMPND 2 MOLECULE: UDP-GALACTOPYRANOSE MUTASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 5.4.99.9; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 573; SOURCE 4 STRAIN: 01 (ATCC 13882); SOURCE 5 GENE: GLF, RFBD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEM-TEASY KEYWDS FLAVOENZYME, PROTEIN-LIGAND COMPLEX, CARBOHYDRATE BIOSYNTHESIS, KEYWDS 2 ISOMERASE, FAD, FLAVOPROTEIN, LIPOPOLYSACCHARIDE BIOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR T.D.GRUBER,L.L.KIESSLING,K.T.FOREST REVDAT 4 06-SEP-23 3INR 1 REMARK REVDAT 3 13-OCT-21 3INR 1 REMARK SEQADV REVDAT 2 13-OCT-09 3INR 1 JRNL REVDAT 1 22-SEP-09 3INR 0 JRNL AUTH T.D.GRUBER,W.M.WESTLER,L.L.KIESSLING,K.T.FOREST JRNL TITL X-RAY CRYSTALLOGRAPHY REVEALS A REDUCED SUBSTRATE COMPLEX OF JRNL TITL 2 UDP-GALACTOPYRANOSE MUTASE POISED FOR COVALENT CATALYSIS BY JRNL TITL 3 FLAVIN . JRNL REF BIOCHEMISTRY V. 48 9171 2009 JRNL REFN ISSN 0006-2960 JRNL PMID 19719175 JRNL DOI 10.1021/BI901437V REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 46068 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) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2421 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3299 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.42 REMARK 3 BIN R VALUE (WORKING SET) : 0.2250 REMARK 3 BIN FREE R VALUE SET COUNT : 173 REMARK 3 BIN FREE R VALUE : 0.3010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6201 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 178 REMARK 3 SOLVENT ATOMS : 287 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.07000 REMARK 3 B22 (A**2) : -1.07000 REMARK 3 B33 (A**2) : 2.14000 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): 0.259 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.208 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.136 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.447 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6559 ; 0.022 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8914 ; 1.811 ; 1.974 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 758 ; 6.467 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 332 ;34.888 ;24.036 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1063 ;15.807 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;18.787 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 930 ; 0.127 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5038 ; 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): 3783 ; 1.103 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6120 ; 2.005 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2776 ; 3.122 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2794 ; 4.745 ; 4.500 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3INR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-AUG-09. REMARK 100 THE DEPOSITION ID IS D_1000054640. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-NOV-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : C(111) DIAMOND LAUE REMARK 200 OPTICS : BERYLLIUM LENS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48652 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08500 REMARK 200 FOR THE DATA SET : 15.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.26600 REMARK 200 FOR SHELL : 7.100 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: 3GF4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DROPS CONTAINING 1.5 MICROLITERS 5 REMARK 280 MG/ML PROTEIN IN 20 MM HEPES WERE COMBINED WITH 1.5 MICROLITERS REMARK 280 WELL SOLUTION (85 MM AMMONIUM ACETATE, 42 MM TRI-SODIUM CITRATE, REMARK 280 12.3% PEG 4000, 7.5% GLYCEROL, 15 MM L-CYSTEINE, 5 MM UDP-GLC) REMARK 280 FOR 1-2 WEEKS. CRYSTALS WERE THEN SOAKED IN A SOLUTION OF 53% REMARK 280 QIAGEN CRYOS SUITE CONDITION #87 WITH 15 MM L-CYS, 30% METHANOL, REMARK 280 90 MM UDP-GALP (24HRS), PH 5.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.29200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 32.14600 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 96.43800 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: 2160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 HIS A 385 REMARK 465 HIS A 386 REMARK 465 HIS A 387 REMARK 465 HIS A 388 REMARK 465 HIS A 389 REMARK 465 HIS A 390 REMARK 465 MET B 1 REMARK 465 ILE B 129 REMARK 465 ALA B 130 REMARK 465 ASP B 131 REMARK 465 PRO B 132 REMARK 465 GLN B 133 REMARK 465 HIS B 385 REMARK 465 HIS B 386 REMARK 465 HIS B 387 REMARK 465 HIS B 388 REMARK 465 HIS B 389 REMARK 465 HIS B 390 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 HIS B 208 O HOH B 513 2.10 REMARK 500 OD1 ASP A 351 O HOH A 427 2.15 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 146 CD GLU A 146 OE1 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 ASP A 182 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG A 280 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 343 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG B 280 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 LEU B 331 CB - CG - CD1 ANGL. DEV. = -17.5 DEGREES REMARK 500 ARG B 343 NE - CZ - NH2 ANGL. DEV. = -3.3 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 PRO A 59 129.69 -37.29 REMARK 500 PHE A 179 33.07 -97.73 REMARK 500 ASN A 373 48.00 39.15 REMARK 500 ASN B 51 19.18 54.59 REMARK 500 ASP B 126 -76.13 -69.57 REMARK 500 SER B 127 -24.17 69.11 REMARK 500 SER B 165 -9.89 -56.15 REMARK 500 SER B 170 171.24 -56.95 REMARK 500 ILE B 171 -58.49 87.62 REMARK 500 PHE B 179 53.94 -93.48 REMARK 500 TYR B 313 -72.24 -104.51 REMARK 500 VAL B 383 -10.47 -142.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FAD A 391 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FAD B 391 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDU A 392 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDU B 392 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1I8T RELATED DB: PDB REMARK 900 UDP-GALACTOPYRANOSE MUTASE FROM E. COLI REMARK 900 RELATED ID: 2BI7 RELATED DB: PDB REMARK 900 UDP-GALACTOPYRANOSE MUTASE FROM K. PNEUMONIAE, OXIDIZED REMARK 900 RELATED ID: 2BI8 RELATED DB: PDB REMARK 900 UDP-GALACTOPYRANOSE MUTASE FROM K. PNEUMONIAE, REDUCED REMARK 900 RELATED ID: 1WAM RELATED DB: PDB REMARK 900 UDP-GALACTOPYRANOSE MUTASE FROM K. PNEUMONIAE, REDUCED REMARK 900 RELATED ID: 1V0J RELATED DB: PDB REMARK 900 UDP-GALACTOPYRANOSE MUTASE FROM M. TUBERCULOSIS REMARK 900 RELATED ID: 3GF4 RELATED DB: PDB REMARK 900 STRUCTURE OF UDP-GALACTOPYRANOSE MUTASE BOUND TO UDP-GLUCOSE REMARK 900 RELATED ID: 3INT RELATED DB: PDB REMARK 900 STRUCTURE OF UDP-GALACTOPYRANOSE MUTASE BOUND TO UDP-GALACTOSE REMARK 900 (REDUCED) REMARK 999 REMARK 999 SEQUENCE REMARK 999 THESE ARE VERY CONSERVATIVE MUTATIONS FROM THE PUBLISHED SEQUENCE. REMARK 999 THEY REFLECT SEQUENCE DIFFERENCES IN THE ISOLATE THAT OUR CLONED REMARK 999 DNA CAME FROM RATHER THAN ERRORS IN THE STRUCTURE OR THE PDB FILE DBREF 3INR A 1 383 UNP Q48485 GLF1_KLEPN 1 383 DBREF 3INR B 1 383 UNP Q48485 GLF1_KLEPN 1 383 SEQADV 3INR ILE A 73 UNP Q48485 VAL 73 SEE REMARK 999 SEQADV 3INR ASP A 222 UNP Q48485 GLU 222 SEE REMARK 999 SEQADV 3INR ILE A 258 UNP Q48485 THR 258 SEE REMARK 999 SEQADV 3INR ASP A 372 UNP Q48485 GLU 372 SEE REMARK 999 SEQADV 3INR GLY A 384 UNP Q48485 ARG 384 ENGINEERED MUTATION SEQADV 3INR HIS A 385 UNP Q48485 EXPRESSION TAG SEQADV 3INR HIS A 386 UNP Q48485 EXPRESSION TAG SEQADV 3INR HIS A 387 UNP Q48485 EXPRESSION TAG SEQADV 3INR HIS A 388 UNP Q48485 EXPRESSION TAG SEQADV 3INR HIS A 389 UNP Q48485 EXPRESSION TAG SEQADV 3INR HIS A 390 UNP Q48485 EXPRESSION TAG SEQADV 3INR ILE B 73 UNP Q48485 VAL 73 SEE REMARK 999 SEQADV 3INR ASP B 222 UNP Q48485 GLU 222 SEE REMARK 999 SEQADV 3INR ILE B 258 UNP Q48485 THR 258 SEE REMARK 999 SEQADV 3INR ASP B 372 UNP Q48485 GLU 372 SEE REMARK 999 SEQADV 3INR GLY B 384 UNP Q48485 ARG 384 ENGINEERED MUTATION SEQADV 3INR HIS B 385 UNP Q48485 EXPRESSION TAG SEQADV 3INR HIS B 386 UNP Q48485 EXPRESSION TAG SEQADV 3INR HIS B 387 UNP Q48485 EXPRESSION TAG SEQADV 3INR HIS B 388 UNP Q48485 EXPRESSION TAG SEQADV 3INR HIS B 389 UNP Q48485 EXPRESSION TAG SEQADV 3INR HIS B 390 UNP Q48485 EXPRESSION TAG SEQRES 1 A 390 MET LYS SER LYS LYS ILE LEU ILE VAL GLY ALA GLY PHE SEQRES 2 A 390 SER GLY ALA VAL ILE GLY ARG GLN LEU ALA GLU LYS GLY SEQRES 3 A 390 HIS GLN VAL HIS ILE ILE ASP GLN ARG ASP HIS ILE GLY SEQRES 4 A 390 GLY ASN SER TYR ASP ALA ARG ASP SER GLU THR ASN VAL SEQRES 5 A 390 MET VAL HIS VAL TYR GLY PRO HIS ILE PHE HIS THR ASP SEQRES 6 A 390 ASN GLU THR VAL TRP ASN TYR ILE ASN LYS HIS ALA GLU SEQRES 7 A 390 MET MET PRO TYR VAL ASN ARG VAL LYS ALA THR VAL ASN SEQRES 8 A 390 GLY GLN VAL PHE SER LEU PRO ILE ASN LEU HIS THR ILE SEQRES 9 A 390 ASN GLN PHE PHE SER LYS THR CYS SER PRO ASP GLU ALA SEQRES 10 A 390 ARG ALA LEU ILE ALA GLU LYS GLY ASP SER THR ILE ALA SEQRES 11 A 390 ASP PRO GLN THR PHE GLU GLU GLN ALA LEU ARG PHE ILE SEQRES 12 A 390 GLY LYS GLU LEU TYR GLU ALA PHE PHE LYS GLY TYR THR SEQRES 13 A 390 ILE LYS GLN TRP GLY MET GLN PRO SER GLU LEU PRO ALA SEQRES 14 A 390 SER ILE LEU LYS ARG LEU PRO VAL ARG PHE ASN TYR ASP SEQRES 15 A 390 ASP ASN TYR PHE ASN HIS LYS PHE GLN GLY MET PRO LYS SEQRES 16 A 390 CYS GLY TYR THR GLN MET ILE LYS SER ILE LEU ASN HIS SEQRES 17 A 390 GLU ASN ILE LYS VAL ASP LEU GLN ARG GLU PHE ILE VAL SEQRES 18 A 390 ASP GLU ARG THR HIS TYR ASP HIS VAL PHE TYR SER GLY SEQRES 19 A 390 PRO LEU ASP ALA PHE TYR GLY TYR GLN TYR GLY ARG LEU SEQRES 20 A 390 GLY TYR ARG THR LEU ASP PHE LYS LYS PHE ILE TYR GLN SEQRES 21 A 390 GLY ASP TYR GLN GLY CYS ALA VAL MET ASN TYR CYS SER SEQRES 22 A 390 VAL ASP VAL PRO TYR THR ARG ILE THR GLU HIS LYS TYR SEQRES 23 A 390 PHE SER PRO TRP GLU GLN HIS ASP GLY SER VAL CYS TYR SEQRES 24 A 390 LYS GLU TYR SER ARG ALA CYS GLU GLU ASN ASP ILE PRO SEQRES 25 A 390 TYR TYR PRO ILE ARG GLN MET GLY GLU MET ALA LEU LEU SEQRES 26 A 390 GLU LYS TYR LEU SER LEU ALA GLU ASN GLU THR ASN ILE SEQRES 27 A 390 THR PHE VAL GLY ARG LEU GLY THR TYR ARG TYR LEU ASP SEQRES 28 A 390 MET ASP VAL THR ILE ALA GLU ALA LEU LYS THR ALA GLU SEQRES 29 A 390 VAL TYR LEU ASN SER LEU THR ASP ASN GLN PRO MET PRO SEQRES 30 A 390 VAL PHE THR VAL SER VAL GLY HIS HIS HIS HIS HIS HIS SEQRES 1 B 390 MET LYS SER LYS LYS ILE LEU ILE VAL GLY ALA GLY PHE SEQRES 2 B 390 SER GLY ALA VAL ILE GLY ARG GLN LEU ALA GLU LYS GLY SEQRES 3 B 390 HIS GLN VAL HIS ILE ILE ASP GLN ARG ASP HIS ILE GLY SEQRES 4 B 390 GLY ASN SER TYR ASP ALA ARG ASP SER GLU THR ASN VAL SEQRES 5 B 390 MET VAL HIS VAL TYR GLY PRO HIS ILE PHE HIS THR ASP SEQRES 6 B 390 ASN GLU THR VAL TRP ASN TYR ILE ASN LYS HIS ALA GLU SEQRES 7 B 390 MET MET PRO TYR VAL ASN ARG VAL LYS ALA THR VAL ASN SEQRES 8 B 390 GLY GLN VAL PHE SER LEU PRO ILE ASN LEU HIS THR ILE SEQRES 9 B 390 ASN GLN PHE PHE SER LYS THR CYS SER PRO ASP GLU ALA SEQRES 10 B 390 ARG ALA LEU ILE ALA GLU LYS GLY ASP SER THR ILE ALA SEQRES 11 B 390 ASP PRO GLN THR PHE GLU GLU GLN ALA LEU ARG PHE ILE SEQRES 12 B 390 GLY LYS GLU LEU TYR GLU ALA PHE PHE LYS GLY TYR THR SEQRES 13 B 390 ILE LYS GLN TRP GLY MET GLN PRO SER GLU LEU PRO ALA SEQRES 14 B 390 SER ILE LEU LYS ARG LEU PRO VAL ARG PHE ASN TYR ASP SEQRES 15 B 390 ASP ASN TYR PHE ASN HIS LYS PHE GLN GLY MET PRO LYS SEQRES 16 B 390 CYS GLY TYR THR GLN MET ILE LYS SER ILE LEU ASN HIS SEQRES 17 B 390 GLU ASN ILE LYS VAL ASP LEU GLN ARG GLU PHE ILE VAL SEQRES 18 B 390 ASP GLU ARG THR HIS TYR ASP HIS VAL PHE TYR SER GLY SEQRES 19 B 390 PRO LEU ASP ALA PHE TYR GLY TYR GLN TYR GLY ARG LEU SEQRES 20 B 390 GLY TYR ARG THR LEU ASP PHE LYS LYS PHE ILE TYR GLN SEQRES 21 B 390 GLY ASP TYR GLN GLY CYS ALA VAL MET ASN TYR CYS SER SEQRES 22 B 390 VAL ASP VAL PRO TYR THR ARG ILE THR GLU HIS LYS TYR SEQRES 23 B 390 PHE SER PRO TRP GLU GLN HIS ASP GLY SER VAL CYS TYR SEQRES 24 B 390 LYS GLU TYR SER ARG ALA CYS GLU GLU ASN ASP ILE PRO SEQRES 25 B 390 TYR TYR PRO ILE ARG GLN MET GLY GLU MET ALA LEU LEU SEQRES 26 B 390 GLU LYS TYR LEU SER LEU ALA GLU ASN GLU THR ASN ILE SEQRES 27 B 390 THR PHE VAL GLY ARG LEU GLY THR TYR ARG TYR LEU ASP SEQRES 28 B 390 MET ASP VAL THR ILE ALA GLU ALA LEU LYS THR ALA GLU SEQRES 29 B 390 VAL TYR LEU ASN SER LEU THR ASP ASN GLN PRO MET PRO SEQRES 30 B 390 VAL PHE THR VAL SER VAL GLY HIS HIS HIS HIS HIS HIS HET FAD A 391 53 HET GDU A 392 36 HET FAD B 391 53 HET GDU B 392 36 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM GDU GALACTOSE-URIDINE-5'-DIPHOSPHATE HETSYN GDU UDP-D-GALACTOPYRANOSE FORMUL 3 FAD 2(C27 H33 N9 O15 P2) FORMUL 4 GDU 2(C15 H24 N2 O17 P2) FORMUL 7 HOH *287(H2 O) HELIX 1 1 GLY A 12 GLU A 24 1 13 HELIX 2 2 GLY A 39 SER A 42 5 4 HELIX 3 3 ASN A 66 LYS A 75 1 10 HELIX 4 4 ASN A 100 PHE A 108 1 9 HELIX 5 5 SER A 113 GLY A 125 1 13 HELIX 6 6 THR A 134 ILE A 143 1 10 HELIX 7 7 GLY A 144 PHE A 152 1 9 HELIX 8 8 PHE A 152 GLY A 161 1 10 HELIX 9 9 GLN A 163 PRO A 168 5 6 HELIX 10 10 ALA A 169 ARG A 174 1 6 HELIX 11 11 CYS A 196 ASN A 207 1 12 HELIX 12 12 ILE A 220 TYR A 227 5 8 HELIX 13 13 PRO A 235 TYR A 240 1 6 HELIX 14 14 LYS A 285 SER A 288 5 4 HELIX 15 15 GLN A 318 GLU A 333 1 16 HELIX 16 16 VAL A 341 TYR A 347 1 7 HELIX 17 17 ASP A 351 ASP A 372 1 22 HELIX 18 18 GLY B 12 GLU B 24 1 13 HELIX 19 19 GLY B 39 SER B 42 5 4 HELIX 20 20 ASN B 66 LYS B 75 1 10 HELIX 21 21 ASN B 100 SER B 109 1 10 HELIX 22 22 SER B 113 GLY B 125 1 13 HELIX 23 23 THR B 134 ILE B 143 1 10 HELIX 24 24 ILE B 143 PHE B 152 1 10 HELIX 25 25 PHE B 152 GLY B 161 1 10 HELIX 26 26 GLN B 163 LEU B 167 5 5 HELIX 27 27 CYS B 196 ASN B 207 1 12 HELIX 28 28 ILE B 220 TYR B 227 5 8 HELIX 29 29 PRO B 235 TYR B 240 1 6 HELIX 30 30 LYS B 285 SER B 288 5 4 HELIX 31 31 GLN B 318 GLU B 333 1 16 HELIX 32 32 VAL B 341 TYR B 347 1 7 HELIX 33 33 ASP B 351 ASP B 372 1 22 SHEET 1 A 5 ILE A 211 ASP A 214 0 SHEET 2 A 5 GLN A 28 ILE A 32 1 N ILE A 31 O LYS A 212 SHEET 3 A 5 LYS A 5 VAL A 9 1 N ILE A 6 O HIS A 30 SHEET 4 A 5 HIS A 229 TYR A 232 1 O PHE A 231 N VAL A 9 SHEET 5 A 5 ILE A 338 PHE A 340 1 O THR A 339 N TYR A 232 SHEET 1 B 2 ASP A 44 ARG A 46 0 SHEET 2 B 2 MET A 53 HIS A 55 -1 O VAL A 54 N ALA A 45 SHEET 1 C 3 PHE A 62 THR A 64 0 SHEET 2 C 3 PHE A 190 PRO A 194 -1 O PHE A 190 N THR A 64 SHEET 3 C 3 MET A 79 PRO A 81 -1 N MET A 80 O MET A 193 SHEET 1 D 7 GLN A 93 SER A 96 0 SHEET 2 D 7 LYS A 87 VAL A 90 -1 N ALA A 88 O PHE A 95 SHEET 3 D 7 VAL A 268 TYR A 271 1 O ASN A 270 N LYS A 87 SHEET 4 D 7 ARG A 280 GLU A 283 -1 O ILE A 281 N MET A 269 SHEET 5 D 7 GLY A 295 ALA A 305 -1 O GLU A 301 N ARG A 280 SHEET 6 D 7 TYR A 249 GLN A 260 -1 N LYS A 255 O LYS A 300 SHEET 7 D 7 TYR A 314 PRO A 315 -1 O TYR A 314 N ARG A 250 SHEET 1 E 5 ILE B 211 ASP B 214 0 SHEET 2 E 5 GLN B 28 ILE B 32 1 N VAL B 29 O LYS B 212 SHEET 3 E 5 LYS B 5 VAL B 9 1 N ILE B 6 O GLN B 28 SHEET 4 E 5 HIS B 229 TYR B 232 1 O PHE B 231 N VAL B 9 SHEET 5 E 5 ILE B 338 PHE B 340 1 O THR B 339 N TYR B 232 SHEET 1 F 2 ASP B 44 ARG B 46 0 SHEET 2 F 2 MET B 53 HIS B 55 -1 O VAL B 54 N ALA B 45 SHEET 1 G 3 PHE B 62 THR B 64 0 SHEET 2 G 3 PHE B 190 PRO B 194 -1 O PHE B 190 N THR B 64 SHEET 3 G 3 MET B 79 PRO B 81 -1 N MET B 80 O MET B 193 SHEET 1 H 7 GLN B 93 SER B 96 0 SHEET 2 H 7 LYS B 87 VAL B 90 -1 N ALA B 88 O PHE B 95 SHEET 3 H 7 VAL B 268 TYR B 271 1 O ASN B 270 N THR B 89 SHEET 4 H 7 ARG B 280 GLU B 283 -1 O ILE B 281 N MET B 269 SHEET 5 H 7 GLY B 295 ALA B 305 -1 O GLU B 301 N ARG B 280 SHEET 6 H 7 TYR B 249 GLN B 260 -1 N TYR B 259 O SER B 296 SHEET 7 H 7 TYR B 314 PRO B 315 -1 O TYR B 314 N ARG B 250 CISPEP 1 LEU A 97 PRO A 98 0 -8.48 CISPEP 2 LEU B 97 PRO B 98 0 -3.19 SITE 1 AC1 36 GLY A 10 GLY A 12 PHE A 13 SER A 14 SITE 2 AC1 36 ASP A 33 GLN A 34 ARG A 35 GLY A 40 SITE 3 AC1 36 ASN A 41 SER A 42 TYR A 57 PRO A 59 SITE 4 AC1 36 HIS A 60 ILE A 61 ARG A 217 PHE A 219 SITE 5 AC1 36 TYR A 232 GLY A 234 PRO A 235 TYR A 313 SITE 6 AC1 36 TYR A 314 GLY A 342 ARG A 343 TYR A 349 SITE 7 AC1 36 LEU A 350 ASP A 351 MET A 352 THR A 355 SITE 8 AC1 36 HOH A 393 HOH A 396 HOH A 419 HOH A 420 SITE 9 AC1 36 HOH A 429 HOH A 483 HOH A 591 HOH A 642 SITE 1 AC2 32 VAL B 9 GLY B 10 GLY B 12 PHE B 13 SITE 2 AC2 32 SER B 14 ASP B 33 GLN B 34 GLY B 40 SITE 3 AC2 32 ASN B 41 PRO B 59 HIS B 60 ILE B 61 SITE 4 AC2 32 ARG B 217 PHE B 219 GLY B 234 PRO B 235 SITE 5 AC2 32 TYR B 313 TYR B 314 GLY B 342 ARG B 343 SITE 6 AC2 32 TYR B 349 LEU B 350 ASP B 351 MET B 352 SITE 7 AC2 32 THR B 355 HOH B 393 HOH B 395 HOH B 402 SITE 8 AC2 32 HOH B 445 HOH B 466 HOH B 534 HOH B 646 SITE 1 AC3 18 LEU A 97 PHE A 135 PHE A 151 PHE A 152 SITE 2 AC3 18 TYR A 155 THR A 156 TRP A 160 ARG A 174 SITE 3 AC3 18 LEU A 175 TYR A 185 ASN A 270 CYS A 272 SITE 4 AC3 18 TYR A 349 ASP A 351 HOH A 667 HOH A 668 SITE 5 AC3 18 HOH A 669 HOH A 670 SITE 1 AC4 16 LEU B 97 PHE B 151 PHE B 152 TYR B 155 SITE 2 AC4 16 THR B 156 TRP B 160 ILE B 171 ARG B 174 SITE 3 AC4 16 LEU B 175 TYR B 185 ASN B 270 TYR B 314 SITE 4 AC4 16 TYR B 349 ASP B 351 HOH B 672 HOH B 674 CRYST1 93.799 93.799 128.584 90.00 90.00 90.00 P 41 8 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 0.010661 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010661 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007777 0.00000