10 20 30 40 50 60 70 80 1I3N - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER ISOMERASE 15-FEB-01 1I3N
TITLE MOLECULAR BASIS FOR SEVERE EPIMERASE-DEFICIENCY TITLE 2 GALACTOSEMIA: X-RAY STRUCTURE OF THE HUMAN V94M- TITLE 3 SUBSTITUTED UDP-GALACTOSE 4-EPIMERASE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: UDP-GLUCOSE 4-EPIMERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: UDP-GALACTOSE 4-EPIMERASE; COMPND 5 EC: 5.1.3.2; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HGALE; SOURCE 6 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: GS115; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PPIC3.5KHGALE
KEYWDS EPIMERASE GALACTOSEMIA SHORT-CHAIN DEHYDROGENASE, ISOMERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR J.B.THODEN,T.M.WOHLERS,J.L.FRIDOVICH-KEIL,H.M.HOLDEN
REVDAT 3 24-FEB-09 1I3N 1 VERSN REVDAT 2 01-APR-03 1I3N 1 JRNL REVDAT 1 20-JUN-01 1I3N 0
JRNL AUTH J.B.THODEN,T.M.WOHLERS,J.L.FRIDOVICH-KEIL, JRNL AUTH 2 H.M.HOLDEN JRNL TITL MOLECULAR BASIS FOR SEVERE EPIMERASE DEFICIENCY JRNL TITL 2 GALACTOSEMIA. X-RAY STRUCTURE OF THE HUMAN JRNL TITL 3 V94M-SUBSTITUTED UDP-GALACTOSE 4-EPIMERASE. JRNL REF J.BIOL.CHEM. V. 276 20617 2001 JRNL REFN ISSN 0021-9258 JRNL PMID 11279193 JRNL DOI 10.1074/JBC.M101304200
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 107109 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 10771 REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.1780 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 107109 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5403 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 172 REMARK 3 SOLVENT ATOMS : 925 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.010 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 2.170 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : ENGH & HUBER REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1I3N COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-FEB-01. REMARK 100 THE RCSB ID CODE IS RCSB012862.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SBC-2 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 107214 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : 97.3 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 37.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.27900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: TNT REMARK 200 STARTING MODEL: PDB ENTERY 1EK6 REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3400, MES, SODIUM CHLORIDE, REMARK 280 MAGNESIUM CHLORIDE, NADH, UDP-GALNAC, PH 6, BATCH, TEMPERATURE REMARK 280 276K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 39.05000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.40000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.40000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.05000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A HOMODIMER REMARK 300 COMPOSED OF CHAINS A & B
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: 7260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -85.0 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 MET B 1 REMARK 465 GLN B 347 REMARK 465 ALA B 348
REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 VAL A 180 CG1 CG2 REMARK 470 VAL B 180 CG1 CG2 REMARK 470 THR B 346 OG1 CG2
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 1766 O HOH B 2021 2.14 REMARK 500 O HOH A 1997 O HOH B 1420 2.16 REMARK 500 OE1 GLN A 70 O HOH A 1996 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 A 21 CD GLU A 21 OE2 0.073 REMARK 500 GLU A 54 CD GLU A 54 OE2 0.093 REMARK 500 GLU A 63 CD GLU A 63 OE2 0.074 REMARK 500 GLU A 117 CD GLU A 117 OE2 0.091 REMARK 500 GLU A 146 CD GLU A 146 OE2 0.075 REMARK 500 GLU A 301 CD GLU A 301 OE2 0.066 REMARK 500 GLU A 316 CD GLU A 316 OE2 0.075 REMARK 500 GLU A 317 CD GLU A 317 OE2 0.073 REMARK 500 GLU B 54 CD GLU B 54 OE2 0.068 REMARK 500 GLU B 146 CD GLU B 146 OE2 0.076 REMARK 500 GLU B 165 CD GLU B 165 OE2 0.066 REMARK 500 GLU B 221 CD GLU B 221 OE2 0.069 REMARK 500 GLU B 285 CD GLU B 285 OE2 0.076 REMARK 500 GLU B 317 CD GLU B 317 OE2 0.076 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 66 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A 66 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP A 69 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP A 69 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 LYS A 100 CB - CA - C ANGL. DEV. = -12.8 DEGREES REMARK 500 ASP A 145 CB - CG - OD2 ANGL. DEV. = -6.4 DEGREES REMARK 500 THR A 154 N - CA - C ANGL. DEV. = 19.4 DEGREES REMARK 500 THR A 154 C - N - CA ANGL. DEV. = 19.5 DEGREES REMARK 500 ASP A 170 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ARG A 184 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 219 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ASP A 231 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP A 234 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ARG A 239 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ASP A 246 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 246 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ARG A 256 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ASP A 327 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP A 327 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ARG A 335 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG B 58 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP B 66 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP B 69 CB - CG - OD1 ANGL. DEV. = 6.9 DEGREES REMARK 500 ASP B 69 CB - CG - OD2 ANGL. DEV. = -8.4 DEGREES REMARK 500 ARG B 75 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG B 75 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 106 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ASP B 145 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ASP B 145 CB - CG - OD2 ANGL. DEV. = -8.2 DEGREES REMARK 500 ASP B 170 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP B 170 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ASP B 200 CB - CG - OD1 ANGL. DEV. = 8.0 DEGREES REMARK 500 ASP B 200 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP B 231 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP B 231 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP B 246 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP B 246 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP B 303 CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG B 328 NE - CZ - NH1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG B 328 NE - CZ - NH2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ASP B 332 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ASP B 332 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG B 335 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 131 -169.92 -103.89 REMARK 500 THR A 154 -90.58 9.32 REMARK 500 PHE A 186 -121.25 -91.64 REMARK 500 GLU B 3 -51.33 -131.00 REMARK 500 MET B 94 36.82 -91.88 REMARK 500 VAL B 124 79.82 -103.74 REMARK 500 LYS B 125 48.40 -98.58 REMARK 500 SER B 131 -167.49 -100.68 REMARK 500 PHE B 186 -117.24 -92.75 REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B1863 DISTANCE = 6.74 ANGSTROMS REMARK 525 HOH A1610 DISTANCE = 6.82 ANGSTROMS REMARK 525 HOH A1950 DISTANCE = 5.13 ANGSTROMS
REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 994 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1463 O REMARK 620 2 HOH A1565 O 96.6 REMARK 620 3 HOH A1953 O 64.4 73.6 REMARK 620 4 SER A 312 OG 139.7 98.3 84.5 REMARK 620 5 HOH A1174 O 123.8 97.0 168.8 91.1 REMARK 620 6 HOH A1954 O 89.3 145.7 78.9 58.7 107.5 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 CL A 990 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 991 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 992 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 993 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 994 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD A 400 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UD1 A 401 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD B 900 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UD1 B 901
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1I3K RELATED DB: PDB REMARK 900 MOLECULAR BASIS FOR SEVERE EPIMERASE-DEFICIENCY REMARK 900 GALACTOSEMIA: X-RAY STRUCTURE OF THE HUMAN V94M-SUBSTITUTED REMARK 900 UDP-GALACTOSE 4-EPIMERASE REMARK 900 RELATED ID: 1I3L RELATED DB: PDB REMARK 900 MOLECULAR BASIS FOR SEVERE EPIMERASE-DEFICIENCY REMARK 900 GALACTOSEMIA: X-RAY STRUCTURE OF THE HUMAN V94M-SUBSTITUTED REMARK 900 UDP-GALACTOSE 4-EPIMERASE REMARK 900 RELATED ID: 1I3M RELATED DB: PDB REMARK 900 MOLECULAR BASIS FOR SEVERE EPIMERASE-DEFICIENCY REMARK 900 GALACTOSEMIA: X-RAY STRUCTURE OF THE HUMAN V94M-SUBSTITUTED REMARK 900 UDP-GALACTOSE 4-EPIMERASE
DBREF 1I3N A 1 348 UNP Q14376 GALE_HUMAN 1 348 DBREF 1I3N B 1 348 UNP Q14376 GALE_HUMAN 1 348
SEQADV 1I3N MET A 94 UNP Q14376 VAL 94 ENGINEERED SEQADV 1I3N MET B 94 UNP Q14376 VAL 94 ENGINEERED
SEQRES 1 A 348 MET ALA GLU LYS VAL LEU VAL THR GLY GLY ALA GLY TYR SEQRES 2 A 348 ILE GLY SER HIS THR VAL LEU GLU LEU LEU GLU ALA GLY SEQRES 3 A 348 TYR LEU PRO VAL VAL ILE ASP ASN PHE HIS ASN ALA PHE SEQRES 4 A 348 ARG GLY GLY GLY SER LEU PRO GLU SER LEU ARG ARG VAL SEQRES 5 A 348 GLN GLU LEU THR GLY ARG SER VAL GLU PHE GLU GLU MET SEQRES 6 A 348 ASP ILE LEU ASP GLN GLY ALA LEU GLN ARG LEU PHE LYS SEQRES 7 A 348 LYS TYR SER PHE MET ALA VAL ILE HIS PHE ALA GLY LEU SEQRES 8 A 348 LYS ALA MET GLY GLU SER VAL GLN LYS PRO LEU ASP TYR SEQRES 9 A 348 TYR ARG VAL ASN LEU THR GLY THR ILE GLN LEU LEU GLU SEQRES 10 A 348 ILE MET LYS ALA HIS GLY VAL LYS ASN LEU VAL PHE SER SEQRES 11 A 348 SER SER ALA THR VAL TYR GLY ASN PRO GLN TYR LEU PRO SEQRES 12 A 348 LEU ASP GLU ALA HIS PRO THR GLY GLY CYS THR ASN PRO SEQRES 13 A 348 TYR GLY LYS SER LYS PHE PHE ILE GLU GLU MET ILE ARG SEQRES 14 A 348 ASP LEU CYS GLN ALA ASP LYS THR TRP ASN VAL VAL LEU SEQRES 15 A 348 LEU ARG TYR PHE ASN PRO THR GLY ALA HIS ALA SER GLY SEQRES 16 A 348 CYS ILE GLY GLU ASP PRO GLN GLY ILE PRO ASN ASN LEU SEQRES 17 A 348 MET PRO TYR VAL SER GLN VAL ALA ILE GLY ARG ARG GLU SEQRES 18 A 348 ALA LEU ASN VAL PHE GLY ASN ASP TYR ASP THR GLU ASP SEQRES 19 A 348 GLY THR GLY VAL ARG ASP TYR ILE HIS VAL VAL ASP LEU SEQRES 20 A 348 ALA LYS GLY HIS ILE ALA ALA LEU ARG LYS LEU LYS GLU SEQRES 21 A 348 GLN CYS GLY CYS ARG ILE TYR ASN LEU GLY THR GLY THR SEQRES 22 A 348 GLY TYR SER VAL LEU GLN MET VAL GLN ALA MET GLU LYS SEQRES 23 A 348 ALA SER GLY LYS LYS ILE PRO TYR LYS VAL VAL ALA ARG SEQRES 24 A 348 ARG GLU GLY ASP VAL ALA ALA CYS TYR ALA ASN PRO SER SEQRES 25 A 348 LEU ALA GLN GLU GLU LEU GLY TRP THR ALA ALA LEU GLY SEQRES 26 A 348 LEU ASP ARG MET CYS GLU ASP LEU TRP ARG TRP GLN LYS SEQRES 27 A 348 GLN ASN PRO SER GLY PHE GLY THR GLN ALA SEQRES 1 B 348 MET ALA GLU LYS VAL LEU VAL THR GLY GLY ALA GLY TYR SEQRES 2 B 348 ILE GLY SER HIS THR VAL LEU GLU LEU LEU GLU ALA GLY SEQRES 3 B 348 TYR LEU PRO VAL VAL ILE ASP ASN PHE HIS ASN ALA PHE SEQRES 4 B 348 ARG GLY GLY GLY SER LEU PRO GLU SER LEU ARG ARG VAL SEQRES 5 B 348 GLN GLU LEU THR GLY ARG SER VAL GLU PHE GLU GLU MET SEQRES 6 B 348 ASP ILE LEU ASP GLN GLY ALA LEU GLN ARG LEU PHE LYS SEQRES 7 B 348 LYS TYR SER PHE MET ALA VAL ILE HIS PHE ALA GLY LEU SEQRES 8 B 348 LYS ALA MET GLY GLU SER VAL GLN LYS PRO LEU ASP TYR SEQRES 9 B 348 TYR ARG VAL ASN LEU THR GLY THR ILE GLN LEU LEU GLU SEQRES 10 B 348 ILE MET LYS ALA HIS GLY VAL LYS ASN LEU VAL PHE SER SEQRES 11 B 348 SER SER ALA THR VAL TYR GLY ASN PRO GLN TYR LEU PRO SEQRES 12 B 348 LEU ASP GLU ALA HIS PRO THR GLY GLY CYS THR ASN PRO SEQRES 13 B 348 TYR GLY LYS SER LYS PHE PHE ILE GLU GLU MET ILE ARG SEQRES 14 B 348 ASP LEU CYS GLN ALA ASP LYS THR TRP ASN VAL VAL LEU SEQRES 15 B 348 LEU ARG TYR PHE ASN PRO THR GLY ALA HIS ALA SER GLY SEQRES 16 B 348 CYS ILE GLY GLU ASP PRO GLN GLY ILE PRO ASN ASN LEU SEQRES 17 B 348 MET PRO TYR VAL SER GLN VAL ALA ILE GLY ARG ARG GLU SEQRES 18 B 348 ALA LEU ASN VAL PHE GLY ASN ASP TYR ASP THR GLU ASP SEQRES 19 B 348 GLY THR GLY VAL ARG ASP TYR ILE HIS VAL VAL ASP LEU SEQRES 20 B 348 ALA LYS GLY HIS ILE ALA ALA LEU ARG LYS LEU LYS GLU SEQRES 21 B 348 GLN CYS GLY CYS ARG ILE TYR ASN LEU GLY THR GLY THR SEQRES 22 B 348 GLY TYR SER VAL LEU GLN MET VAL GLN ALA MET GLU LYS SEQRES 23 B 348 ALA SER GLY LYS LYS ILE PRO TYR LYS VAL VAL ALA ARG SEQRES 24 B 348 ARG GLU GLY ASP VAL ALA ALA CYS TYR ALA ASN PRO SER SEQRES 25 B 348 LEU ALA GLN GLU GLU LEU GLY TRP THR ALA ALA LEU GLY SEQRES 26 B 348 LEU ASP ARG MET CYS GLU ASP LEU TRP ARG TRP GLN LYS SEQRES 27 B 348 GLN ASN PRO SER GLY PHE GLY THR GLN ALA
HET CL A 990 1 HET CL B 991 1 HET CL A 992 1 HET CL B 993 1 HET MG A 994 1 HET NAD A 400 44 HET UD1 A 401 40 HET NAD B 900 44 HET UD1 B 901 39
HETNAM CL CHLORIDE ION HETNAM MG MAGNESIUM ION HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM UD1 URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
FORMUL 3 CL 4(CL 1-) FORMUL 7 MG MG 2+ FORMUL 8 NAD 2(C21 H27 N7 O14 P2) FORMUL 9 UD1 2(C17 H27 N3 O17 P2) FORMUL 12 HOH *925(H2 O)
HELIX 1 1 GLY A 12 ALA A 25 1 14 HELIX 2 2 PRO A 46 GLY A 57 1 12 HELIX 3 3 ASP A 69 TYR A 80 1 12 HELIX 4 4 LYS A 100 ASN A 108 1 9 HELIX 5 5 ASN A 108 HIS A 122 1 15 HELIX 6 6 THR A 134 GLY A 137 5 4 HELIX 7 7 ASN A 155 ASP A 175 1 21 HELIX 8 8 ASN A 207 ILE A 217 1 11 HELIX 9 9 VAL A 244 LYS A 259 1 16 HELIX 10 10 VAL A 277 GLY A 289 1 13 HELIX 11 11 PRO A 311 GLU A 317 1 7 HELIX 12 12 GLY A 325 ASN A 340 1 16 HELIX 13 13 GLY B 12 ALA B 25 1 14 HELIX 14 14 PRO B 46 GLY B 57 1 12 HELIX 15 15 ASP B 69 TYR B 80 1 12 HELIX 16 16 GLU B 96 GLN B 99 5 4 HELIX 17 17 LYS B 100 HIS B 122 1 23 HELIX 18 18 THR B 134 GLY B 137 5 4 HELIX 19 19 ASN B 155 ASP B 175 1 21 HELIX 20 20 ASN B 207 ILE B 217 1 11 HELIX 21 21 VAL B 244 GLU B 260 1 17 HELIX 22 22 VAL B 277 GLY B 289 1 13 HELIX 23 23 PRO B 311 LEU B 318 1 8 HELIX 24 24 GLY B 325 ASN B 340 1 16
SHEET 1 A 7 GLU A 61 GLU A 64 0 SHEET 2 A 7 PRO A 29 ASP A 33 1 O PRO A 29 N GLU A 61 SHEET 3 A 7 LYS A 4 THR A 8 1 O VAL A 5 N VAL A 30 SHEET 4 A 7 PHE A 82 HIS A 87 1 N MET A 83 O LYS A 4 SHEET 5 A 7 ASN A 126 SER A 132 1 O ASN A 126 N VAL A 85 SHEET 6 A 7 ASN A 179 TYR A 185 1 O ASN A 179 N LEU A 127 SHEET 7 A 7 CYS A 264 LEU A 269 1 N ARG A 265 O VAL A 180 SHEET 1 B 2 ASN A 187 THR A 189 0 SHEET 2 B 2 TYR A 241 HIS A 243 1 O ILE A 242 N THR A 189 SHEET 1 C 2 LEU A 223 PHE A 226 0 SHEET 2 C 2 TYR A 294 VAL A 297 1 O LYS A 295 N VAL A 225 SHEET 1 D 3 TYR A 275 SER A 276 0 SHEET 2 D 3 VAL A 238 ARG A 239 -1 O ARG A 239 N TYR A 275 SHEET 3 D 3 ALA A 306 CYS A 307 1 N CYS A 307 O VAL A 238 SHEET 1 E 7 GLU B 61 GLU B 64 0 SHEET 2 E 7 PRO B 29 ASP B 33 1 O PRO B 29 N GLU B 61 SHEET 3 E 7 LYS B 4 THR B 8 1 O VAL B 5 N VAL B 30 SHEET 4 E 7 PHE B 82 HIS B 87 1 N MET B 83 O LYS B 4 SHEET 5 E 7 ASN B 126 SER B 132 1 O ASN B 126 N VAL B 85 SHEET 6 E 7 ASN B 179 TYR B 185 1 O ASN B 179 N LEU B 127 SHEET 7 E 7 CYS B 264 LEU B 269 1 O ARG B 265 N LEU B 182 SHEET 1 F 2 ASN B 187 THR B 189 0 SHEET 2 F 2 TYR B 241 HIS B 243 1 O ILE B 242 N THR B 189 SHEET 1 G 2 LEU B 223 PHE B 226 0 SHEET 2 G 2 TYR B 294 VAL B 297 1 O LYS B 295 N VAL B 225 SHEET 1 H 3 TYR B 275 SER B 276 0 SHEET 2 H 3 VAL B 238 ARG B 239 -1 O ARG B 239 N TYR B 275 SHEET 3 H 3 ALA B 306 CYS B 307 1 N CYS B 307 O VAL B 238
LINK MG MG A 994 O HOH A1463 1555 1555 2.26 LINK MG MG A 994 O HOH A1565 1555 1555 2.07 LINK MG MG A 994 O HOH A1953 1555 1555 2.23 LINK MG MG A 994 OG SER A 312 1555 1555 2.27 LINK MG MG A 994 O HOH A1174 1555 1555 2.18 LINK MG MG A 994 O HOH A1954 1555 1555 2.80
CISPEP 1 LEU A 142 PRO A 143 0 -3.25 CISPEP 2 LEU B 142 PRO B 143 0 0.24
SITE 1 AC1 4 GLY A 43 SER A 44 LEU A 45 HOH A1949 SITE 1 AC2 4 LYS A 120 HOH A1438 HOH A1641 LEU B 102 SITE 1 AC3 1 ASP A 231 SITE 1 AC4 3 SER B 44 LEU B 45 ARG B 50 SITE 1 AC5 6 SER A 312 HOH A1174 HOH A1463 HOH A1565 SITE 2 AC5 6 HOH A1953 HOH A1954 SITE 1 AC6 35 GLY A 9 GLY A 12 TYR A 13 ILE A 14 SITE 2 AC6 35 ASP A 33 ASN A 34 HIS A 36 ASN A 37 SITE 3 AC6 35 ALA A 38 MET A 65 ASP A 66 ILE A 67 SITE 4 AC6 35 PHE A 88 ALA A 89 GLY A 90 LYS A 92 SITE 5 AC6 35 VAL A 107 SER A 130 SER A 131 SER A 132 SITE 6 AC6 35 TYR A 157 LYS A 161 TYR A 185 PRO A 188 SITE 7 AC6 35 HOH A1101 HOH A1111 HOH A1113 HOH A1152 SITE 8 AC6 35 HOH A1153 HOH A1347 HOH A1359 HOH A1388 SITE 9 AC6 35 HOH A1788 HOH A1789 HOH A1934 SITE 1 AC7 22 ALA A 93 ASN A 187 ASN A 206 ASN A 207 SITE 2 AC7 22 LEU A 208 ASN A 224 VAL A 225 PHE A 226 SITE 3 AC7 22 GLY A 237 ARG A 239 TYR A 241 VAL A 277 SITE 4 AC7 22 ARG A 300 GLY A 302 ASP A 303 VAL A 304 SITE 5 AC7 22 HOH A1194 HOH A1483 HOH A1504 HOH A1510 SITE 6 AC7 22 HOH A1819 HOH A1926 SITE 1 AC8 32 GLY B 9 GLY B 12 TYR B 13 ILE B 14 SITE 2 AC8 32 ASP B 33 ASN B 34 HIS B 36 ASN B 37 SITE 3 AC8 32 ALA B 38 MET B 65 ASP B 66 ILE B 67 SITE 4 AC8 32 PHE B 88 ALA B 89 GLY B 90 LYS B 92 SITE 5 AC8 32 SER B 130 SER B 131 TYR B 157 LYS B 161 SITE 6 AC8 32 TYR B 185 PRO B 188 UD1 B 901 HOH B1246 SITE 7 AC8 32 HOH B1252 HOH B1264 HOH B1276 HOH B1277 SITE 8 AC8 32 HOH B1589 HOH B1601 HOH B1837 HOH B1935 SITE 1 AC9 21 TYR B 157 ASN B 187 ASN B 206 ASN B 207 SITE 2 AC9 21 LEU B 208 ASN B 224 VAL B 225 PHE B 226 SITE 3 AC9 21 GLY B 237 ARG B 239 TYR B 241 VAL B 277 SITE 4 AC9 21 ARG B 300 ASP B 303 NAD B 900 HOH B1695 SITE 5 AC9 21 HOH B1698 HOH B1716 HOH B1906 HOH B1940 SITE 6 AC9 21 HOH B1985
CRYST1 78.100 90.000 96.800 90.00 90.00 90.00 P 21 21 21 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 0.012804 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011111 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010331 0.00000