HEADER ISOMERASE 05-DEC-09 3KYB TITLE STRUCTURE OF UDP-GALACTOPYRANOSE MUTASE BOUND TO FLAVIN MONONUCLEOTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE 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, FAD, KEYWDS 2 FLAVOPROTEIN, LIPOPOLYSACCHARIDE BIOSYNTHESIS, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR T.D.GRUBER,M.C.DIMOND,L.L.KIESSLING,K.T.FOREST REVDAT 2 13-OCT-21 3KYB 1 REMARK SEQADV REVDAT 1 15-DEC-10 3KYB 0 JRNL AUTH T.D.GRUBER,M.C.DIMOND,L.L.KIESSLING,K.T.FOREST JRNL TITL STRUCTURE OF UDP-GALACTOPYRANOSE MUTASE BOUND TO FLAVIN JRNL TITL 2 MONONUCLEOTIDE JRNL REF TO BE PUBLISHED JRNL REFN 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)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 46820 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 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 : 2499 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) : 3388 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.67 REMARK 3 BIN R VALUE (WORKING SET) : 0.2070 REMARK 3 BIN FREE R VALUE SET COUNT : 178 REMARK 3 BIN FREE R VALUE : 0.3140 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6227 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 230 REMARK 3 SOLVENT ATOMS : 294 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.71000 REMARK 3 B22 (A**2) : -0.71000 REMARK 3 B33 (A**2) : 1.42000 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): 0.250 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.197 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.131 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.245 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6642 ; 0.025 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9037 ; 2.007 ; 1.981 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 762 ; 6.697 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 334 ;35.137 ;24.072 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1067 ;16.464 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;16.900 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 928 ; 0.140 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5116 ; 0.011 ; 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): 3800 ; 1.229 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6150 ; 2.215 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2842 ; 3.469 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2887 ; 5.403 ; 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 3KYB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1000056599. 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) : 0.97857 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 : 49472 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09300 REMARK 200 FOR THE DATA SET : 17.0000 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.28600 REMARK 200 FOR SHELL : 7.200 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: PDB ENTRY 3GF4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.72 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 PH 7.0 WERE COMBINED WITH 1.5 REMARK 280 MICROLITERS WELL SOLUTION (85 MM AMMONIUM ACETATE, 42 MM TRI- REMARK 280 SODIUM CITRATE, 12.3% PEG 4000, 7.5% GLYCEROL, 15 MM L-CYSTEINE, REMARK 280 5 MM UDP-GLC) FOR 1-2 WEEKS. CRYSTAL WAS THEN SOAKED IN A REMARK 280 SOLUTION OF 53% QIAGEN CRYOS SUITE CONDITION #87 WITH 15 MM L- REMARK 280 CYS AND 23 MM FLAVIN MONONUCLEOTIDE (24HRS). CRYSTAL WAS BRIEFLY REMARK 280 SOAKED (20 SECONDS) IN A SOLUTION OF 53% QIAGEN CRYOS SUITE REMARK 280 CONDITION #87 WITH 15 MM L-CYS, 30% METHANOL, 10 MM FLAVIN REMARK 280 MONONUCLEOTIDE PRIOR TO VITRIFICATION, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K, PH 5.6 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 64.40000 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 32.20000 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 96.60000 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: 2140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 VAL B 383 REMARK 465 GLY B 384 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 NE ARG B 118 O HOH B 510 1.98 REMARK 500 OE1 GLN B 159 O1P FMN B 393 2.03 REMARK 500 O HOH B 456 O HOH B 542 2.11 REMARK 500 O HOH B 398 O HOH B 481 2.14 REMARK 500 OH TYR B 232 O HOH B 430 2.17 REMARK 500 ND2 ASN A 184 O PHE A 186 2.19 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 B 218 CB GLU B 218 CG 0.115 REMARK 500 TYR B 249 CE2 TYR B 249 CD2 0.098 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 85 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 85 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 SER A 96 N - CA - CB ANGL. DEV. = -10.1 DEGREES REMARK 500 MET A 193 CG - SD - CE ANGL. DEV. = -14.9 DEGREES REMARK 500 ARG A 250 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG A 250 NE - CZ - NH2 ANGL. DEV. = -7.5 DEGREES REMARK 500 ARG A 304 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 348 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP A 351 CB - CG - OD2 ANGL. DEV. = -7.3 DEGREES REMARK 500 ARG B 250 NE - CZ - NH2 ANGL. DEV. = -3.2 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 PHE A 179 33.70 -96.39 REMARK 500 TYR A 313 -73.28 -103.51 REMARK 500 PHE B 179 48.73 -96.20 REMARK 500 TYR B 240 35.65 -97.19 REMARK 500 TYR B 313 -79.15 -107.19 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 FMN A 392 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FAD B 391 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN B 392 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN B 393 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN B 394 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3INT RELATED DB: PDB REMARK 900 STRUCTURE OF UDP-GALACTOPYRANOSE MUTASE BOUND TO UDP-GALACTOSE REMARK 900 (REDUCED) REMARK 900 RELATED ID: 3INR RELATED DB: PDB REMARK 900 STRUCTURE OF UDP-GALACTOPYRANOSE MUTASE BOUND TO UDP-GALACTOSE REMARK 900 (OXIDIZED) REMARK 900 RELATED ID: 3GF4 RELATED DB: PDB REMARK 900 STRUCTURE OF UDP-GALACTOPYRANOSE MUTASE BOUND TO UDP-GLUCOSE REMARK 900 RELATED ID: 2BI7 RELATED DB: PDB REMARK 900 UDP-GALACTOPYRANOSE MUTASE FROM KLEBSIELLA PNEUMONIAE OXIDISED FAD REMARK 900 RELATED ID: 2BI8 RELATED DB: PDB REMARK 900 UDP-GALACTOPYRANOSE MUTASE FROM KLEBSIELLA PNEUMONIAE WITH REDUCED REMARK 900 FAD REMARK 900 RELATED ID: 1WAM RELATED DB: PDB REMARK 900 STRUCTURE OF UDP-GALACTOPYRANOSE MUTASE FROM KLEBSIELLA PNEUMONIAE REMARK 900 WITH FADH- 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 3KYB A 1 384 UNP Q48485 GLF1_KLEPN 1 384 DBREF 3KYB B 1 384 UNP Q48485 GLF1_KLEPN 1 384 SEQADV 3KYB ILE A 73 UNP Q48485 VAL 73 SEE REMARK 999 SEQADV 3KYB ASP A 222 UNP Q48485 GLU 222 SEE REMARK 999 SEQADV 3KYB ILE A 258 UNP Q48485 THR 258 SEE REMARK 999 SEQADV 3KYB ASP A 372 UNP Q48485 GLU 372 SEE REMARK 999 SEQADV 3KYB GLY A 384 UNP Q48485 ARG 384 ENGINEERED MUTATION SEQADV 3KYB HIS A 385 UNP Q48485 EXPRESSION TAG SEQADV 3KYB HIS A 386 UNP Q48485 EXPRESSION TAG SEQADV 3KYB HIS A 387 UNP Q48485 EXPRESSION TAG SEQADV 3KYB HIS A 388 UNP Q48485 EXPRESSION TAG SEQADV 3KYB HIS A 389 UNP Q48485 EXPRESSION TAG SEQADV 3KYB HIS A 390 UNP Q48485 EXPRESSION TAG SEQADV 3KYB ILE B 73 UNP Q48485 VAL 73 SEE REMARK 999 SEQADV 3KYB ASP B 222 UNP Q48485 GLU 222 SEE REMARK 999 SEQADV 3KYB ILE B 258 UNP Q48485 THR 258 SEE REMARK 999 SEQADV 3KYB ASP B 372 UNP Q48485 GLU 372 SEE REMARK 999 SEQADV 3KYB GLY B 384 UNP Q48485 ARG 384 ENGINEERED MUTATION SEQADV 3KYB HIS B 385 UNP Q48485 EXPRESSION TAG SEQADV 3KYB HIS B 386 UNP Q48485 EXPRESSION TAG SEQADV 3KYB HIS B 387 UNP Q48485 EXPRESSION TAG SEQADV 3KYB HIS B 388 UNP Q48485 EXPRESSION TAG SEQADV 3KYB HIS B 389 UNP Q48485 EXPRESSION TAG SEQADV 3KYB 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 FMN A 392 31 HET FAD B 391 53 HET FMN B 392 31 HET FMN B 393 31 HET FMN B 394 31 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM FMN FLAVIN MONONUCLEOTIDE HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 3 FAD 2(C27 H33 N9 O15 P2) FORMUL 4 FMN 4(C17 H21 N4 O9 P) FORMUL 9 HOH *294(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 SER A 109 1 10 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 ASN A 373 1 23 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 PHE B 152 1 19 HELIX 24 24 PHE B 152 GLY B 161 1 10 HELIX 25 25 GLN B 163 LEU B 167 5 5 HELIX 26 26 PRO B 168 LEU B 172 5 5 HELIX 27 27 CYS B 196 LEU B 206 1 11 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 LEU A 215 0 SHEET 2 A 5 GLN A 28 ASP A 33 1 N ILE A 31 O LYS A 212 SHEET 3 A 5 LYS A 5 VAL A 9 1 N ILE A 8 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 LEU A 97 0 SHEET 2 D 7 VAL A 86 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 TYR A 299 N THR A 282 SHEET 6 D 7 TYR A 249 GLN A 260 -1 N PHE A 257 O CYS A 298 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 ILE B 31 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 LEU B 97 0 SHEET 2 H 7 VAL B 86 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 LYS B 87 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 THR B 251 O ARG B 304 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 -2.10 CISPEP 2 LEU B 97 PRO B 98 0 -2.32 SITE 1 AC1 38 VAL A 9 GLY A 10 GLY A 12 PHE A 13 SITE 2 AC1 38 SER A 14 ASP A 33 GLN A 34 ARG A 35 SITE 3 AC1 38 GLY A 40 ASN A 41 SER A 42 PRO A 59 SITE 4 AC1 38 HIS A 60 ILE A 61 ARG A 217 PHE A 219 SITE 5 AC1 38 TYR A 232 SER A 233 GLY A 234 PRO A 235 SITE 6 AC1 38 LEU A 252 TYR A 313 TYR A 314 GLY A 342 SITE 7 AC1 38 ARG A 343 TYR A 349 LEU A 350 ASP A 351 SITE 8 AC1 38 MET A 352 THR A 355 HOH A 394 HOH A 398 SITE 9 AC1 38 HOH A 403 HOH A 421 HOH A 432 HOH A 465 SITE 10 AC1 38 HOH A 477 HOH A 497 SITE 1 AC2 8 GLN A 159 TRP A 160 ARG A 174 TYR A 185 SITE 2 AC2 8 ARG A 280 TYR A 314 TYR A 349 HOH A 498 SITE 1 AC3 37 VAL B 9 GLY B 10 GLY B 12 PHE B 13 SITE 2 AC3 37 SER B 14 ASP B 33 GLN B 34 ARG B 35 SITE 3 AC3 37 GLY B 40 ASN B 41 PRO B 59 HIS B 60 SITE 4 AC3 37 ILE B 61 ARG B 217 PHE B 219 SER B 233 SITE 5 AC3 37 GLY B 234 PRO B 235 TYR B 313 TYR B 314 SITE 6 AC3 37 GLY B 342 ARG B 343 TYR B 349 LEU B 350 SITE 7 AC3 37 ASP B 351 MET B 352 THR B 355 HOH B 396 SITE 8 AC3 37 HOH B 399 HOH B 405 HOH B 406 HOH B 407 SITE 9 AC3 37 HOH B 426 HOH B 435 HOH B 440 HOH B 474 SITE 10 AC3 37 HOH B 535 SITE 1 AC4 9 GLN B 159 TRP B 160 TYR B 185 HIS B 188 SITE 2 AC4 9 FMN B 393 FMN B 394 HOH B 442 HOH B 462 SITE 3 AC4 9 HOH B 511 SITE 1 AC5 10 TYR B 155 GLN B 159 TRP B 160 TYR B 185 SITE 2 AC5 10 TYR B 314 TYR B 349 FMN B 392 HOH B 417 SITE 3 AC5 10 HOH B 511 HOH B 546 SITE 1 AC6 13 PRO B 98 PHE B 151 PHE B 152 THR B 156 SITE 2 AC6 13 ILE B 171 ARG B 174 PRO B 176 ARG B 178 SITE 3 AC6 13 ASN B 187 FMN B 392 HOH B 418 HOH B 457 SITE 4 AC6 13 HOH B 476 CRYST1 93.800 93.800 128.800 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 0.007764 0.00000 MASTER 404 0 6 33 34 0 32 6 0 0 0 60 END