PDB Short entry for 1I3L HEADER ISOMERASE 15-FEB-01 1I3L TITLE MOLECULAR BASIS FOR SEVERE EPIMERASE-DEFICIENCY GALACTOSEMIA: X-RAY TITLE 2 STRUCTURE OF THE HUMAN V94M-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_VECTOR_TYPE: PLASMID; SOURCE 9 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 6 09-AUG-23 1I3L 1 REMARK REVDAT 5 27-OCT-21 1I3L 1 REMARK SEQADV LINK REVDAT 4 20-NOV-19 1I3L 1 LINK REVDAT 3 24-FEB-09 1I3L 1 VERSN REVDAT 2 01-APR-03 1I3L 1 JRNL REVDAT 1 20-JUN-01 1I3L 0 JRNL AUTH J.B.THODEN,T.M.WOHLERS,J.L.FRIDOVICH-KEIL,H.M.HOLDEN JRNL TITL MOLECULAR BASIS FOR SEVERE EPIMERASE DEFICIENCY JRNL TITL 2 GALACTOSEMIA. X-RAY STRUCTURE OF THE HUMAN V94M-SUBSTITUTED JRNL TITL 3 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 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 (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 107191 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) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 10719 REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.1810 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) : 107191 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5355 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 172 REMARK 3 SOLVENT ATOMS : 935 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) : 2.210 ; 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 : ISOTROPIC REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1I3L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-FEB-01. REMARK 100 THE DEPOSITION ID IS D_1000012860. 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 : 107566 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 (%) : 97.4 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 40.0000 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 (%) : 86.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.24000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.300 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 ENTRY 1EK6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.46 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-GAL , PH 6, BATCH, TEMPERATURE 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 48.50000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.90000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.50000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.05000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.90000 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: 6960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -84.0 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 1213 O HOH B 1885 4555 2.08 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 OE2 0.072 REMARK 500 GLU A 301 CD GLU A 301 OE2 0.068 REMARK 500 GLU A 316 CD GLU A 316 OE2 0.066 REMARK 500 GLU B 146 CD GLU B 146 OE2 0.081 REMARK 500 GLU B 165 CD GLU B 165 OE2 0.071 REMARK 500 GLU B 166 CD GLU B 166 OE2 0.066 REMARK 500 GLU B 260 CD GLU B 260 OE2 0.070 REMARK 500 GLU B 301 CD GLU B 301 OE2 0.070 REMARK 500 GLU B 317 CD GLU B 317 OE2 0.088 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 ALA A 2 CB - CA - C ANGL. DEV. = 10.4 DEGREES REMARK 500 ASP A 66 CB - CG - OD1 ANGL. DEV. = 6.9 DEGREES REMARK 500 ASP A 66 CB - CG - OD2 ANGL. DEV. = -7.3 DEGREES REMARK 500 ALA A 93 C - N - CA ANGL. DEV. = -18.2 DEGREES REMARK 500 ASP A 145 CB - CG - OD2 ANGL. DEV. = -7.0 DEGREES REMARK 500 ARG A 184 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ASP A 234 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP A 246 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ASP A 246 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ASP A 303 CB - CG - OD2 ANGL. DEV. = -7.5 DEGREES REMARK 500 ASP A 327 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASP A 327 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ASP A 332 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG A 335 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 50 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ASP B 66 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ASP B 69 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP B 69 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 TYR B 80 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ALA B 93 N - CA - CB ANGL. DEV. = 10.0 DEGREES REMARK 500 ASP B 145 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES REMARK 500 ASP B 145 CB - CG - OD2 ANGL. DEV. = -8.4 DEGREES REMARK 500 ASP B 200 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ASP B 231 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASP B 246 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ARG B 300 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ASP B 327 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ARG B 335 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 37 43.32 -141.74 REMARK 500 MET A 94 36.43 -97.51 REMARK 500 PHE A 186 -117.21 -93.86 REMARK 500 ASN B 37 42.89 -140.44 REMARK 500 LYS B 125 50.20 -99.99 REMARK 500 SER B 131 -167.72 -103.61 REMARK 500 PHE B 186 -115.79 -92.44 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 993 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 312 OG REMARK 620 2 HOH A1642 O 84.0 REMARK 620 3 HOH A1702 O 119.1 85.3 REMARK 620 4 HOH A1703 O 106.0 170.0 90.7 REMARK 620 5 HOH B1408 O 151.2 85.1 86.5 85.4 REMARK 620 6 HOH B1446 O 69.3 87.4 168.1 94.9 83.6 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 GDU A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDU B 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 990 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 991 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 992 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 993 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD B 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 980 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 981 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1I3K RELATED DB: PDB REMARK 900 MOLECULAR BASIS FOR SEVERE EPIMERASE-DEFICIENCY GALACTOSEMIA: X-RAY REMARK 900 STRUCTURE OF THE HUMAN V94M-SUBSTITUTED UDP-GALACTOSE 4-EPIMERASE REMARK 900 RELATED ID: 1I3M RELATED DB: PDB REMARK 900 MOLECULAR BASIS FOR SEVERE EPIMERASE-DEFICIENCY GALACTOSEMIA: X-RAY REMARK 900 STRUCTURE OF THE HUMAN V94M-SUBSTITUTED UDP-GALACTOSE 4-EPIMERASE REMARK 900 RELATED ID: 1I3N RELATED DB: PDB REMARK 900 MOLECULAR BASIS FOR SEVERE EPIMERASE-DEFICIENCY GALACTOSEMIA: X-RAY REMARK 900 STRUCTURE OF THE HUMAN V94M-SUBSTIRUTED UDP-GALACTOSE 4-EPIMERASE DBREF 1I3L A 1 348 UNP Q14376 GALE_HUMAN 1 348 DBREF 1I3L B 1 348 UNP Q14376 GALE_HUMAN 1 348 SEQADV 1I3L MET A 94 UNP Q14376 VAL 94 ENGINEERED MUTATION SEQADV 1I3L MET B 94 UNP Q14376 VAL 94 ENGINEERED MUTATION 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 GDU A 401 36 HET CL A 990 1 HET MG A 993 1 HET NAD A 400 44 HET EDO A 980 4 HET GDU B 901 36 HET CL B 991 1 HET CL B 992 1 HET NAD B 900 44 HET EDO B 981 4 HETNAM GDU GALACTOSE-URIDINE-5'-DIPHOSPHATE HETNAM CL CHLORIDE ION HETNAM MG MAGNESIUM ION HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM EDO 1,2-ETHANEDIOL HETSYN GDU UDP-D-GALACTOPYRANOSE HETSYN EDO ETHYLENE GLYCOL FORMUL 3 GDU 2(C15 H24 N2 O17 P2) FORMUL 4 CL 3(CL 1-) FORMUL 5 MG MG 2+ FORMUL 6 NAD 2(C21 H27 N7 O14 P2) FORMUL 7 EDO 2(C2 H6 O2) FORMUL 13 HOH *935(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 LYS B 100 HIS B 122 1 23 HELIX 17 17 THR B 134 GLY B 137 5 4 HELIX 18 18 ASN B 155 ASP B 175 1 21 HELIX 19 19 ASN B 207 ILE B 217 1 11 HELIX 20 20 VAL B 244 LYS B 259 1 16 HELIX 21 21 VAL B 277 GLY B 289 1 13 HELIX 22 22 PRO B 311 LEU B 318 1 8 HELIX 23 23 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 O ARG A 265 N LEU A 182 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 N ILE B 242 O ASN B 187 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 OG SER A 312 MG MG A 993 1555 1555 1.99 LINK MG MG A 993 O HOH A1642 1555 1555 2.36 LINK MG MG A 993 O HOH A1702 1555 1555 2.20 LINK MG MG A 993 O HOH A1703 1555 1555 1.89 LINK MG MG A 993 O HOH B1408 1555 2565 2.16 LINK MG MG A 993 O HOH B1446 1555 2565 2.52 CISPEP 1 LEU A 142 PRO A 143 0 -3.21 CISPEP 2 LEU B 142 PRO B 143 0 -0.09 SITE 1 AC1 20 ASN A 155 ASN A 187 ASN A 206 ASN A 207 SITE 2 AC1 20 LEU A 208 ASN A 224 VAL A 225 PHE A 226 SITE 3 AC1 20 GLY A 237 ARG A 239 TYR A 241 VAL A 277 SITE 4 AC1 20 ARG A 300 ASP A 303 HOH A1145 HOH A1322 SITE 5 AC1 20 HOH A1374 HOH A1397 HOH A1551 HOH A1968 SITE 1 AC2 20 ALA B 93 THR B 134 ASN B 187 ASN B 206 SITE 2 AC2 20 ASN B 207 LEU B 208 ASN B 224 VAL B 225 SITE 3 AC2 20 PHE B 226 GLY B 237 ARG B 239 TYR B 241 SITE 4 AC2 20 VAL B 277 ARG B 300 ASP B 303 HOH B1107 SITE 5 AC2 20 HOH B1111 HOH B1367 HOH B1764 HOH B1976 SITE 1 AC3 5 LYS A 100 PRO A 101 LEU A 102 LYS B 120 SITE 2 AC3 5 HOH B1421 SITE 1 AC4 3 HOH A1571 PRO B 101 LEU B 102 SITE 1 AC5 7 GLY B 270 PRO B 311 TRP B 320 THR B 321 SITE 2 AC5 7 ALA B 322 HOH B1139 HOH B1261 SITE 1 AC6 6 SER A 312 HOH A1642 HOH A1702 HOH A1703 SITE 2 AC6 6 HOH B1408 HOH B1446 SITE 1 AC7 35 GLY A 9 GLY A 12 TYR A 13 ILE A 14 SITE 2 AC7 35 ASP A 33 ASN A 34 PHE A 35 HIS A 36 SITE 3 AC7 35 ASN A 37 ALA A 38 MET A 65 ASP A 66 SITE 4 AC7 35 ILE A 67 PHE A 88 ALA A 89 GLY A 90 SITE 5 AC7 35 LYS A 92 VAL A 107 SER A 130 SER A 131 SITE 6 AC7 35 SER A 132 TYR A 157 LYS A 161 TYR A 185 SITE 7 AC7 35 PRO A 188 HOH A1119 HOH A1120 HOH A1138 SITE 8 AC7 35 HOH A1161 HOH A1364 HOH A1388 HOH A1394 SITE 9 AC7 35 HOH A1478 HOH A1578 HOH A1970 SITE 1 AC8 29 GLY B 9 GLY B 12 TYR B 13 ILE B 14 SITE 2 AC8 29 ASP B 33 ASN B 34 HIS B 36 ASN B 37 SITE 3 AC8 29 MET B 65 ASP B 66 ILE B 67 PHE B 88 SITE 4 AC8 29 ALA B 89 GLY B 90 LYS B 92 SER B 130 SITE 5 AC8 29 SER B 131 SER B 132 TYR B 157 LYS B 161 SITE 6 AC8 29 TYR B 185 PRO B 188 HOH B1105 HOH B1109 SITE 7 AC8 29 HOH B1117 HOH B1134 HOH B1146 HOH B1150 SITE 8 AC8 29 HOH B1535 SITE 1 AC9 2 GLY A 42 GLY A 43 SITE 1 BC1 3 ILE B 204 HOH B1296 HOH B1363 CRYST1 78.100 89.800 97.000 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 0.011136 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010309 0.00000