HEADER TRANSFERASE 21-APR-11 3RMV TITLE CRYSTAL STRUCTURE OF HUMAN GLYCOGENIN-1 (GYG1) T83M MUTANT COMPLEXED TITLE 2 WITH MANGANESE AND UDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCOGENIN-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-262; COMPND 5 SYNONYM: GN-1, GN1; COMPND 6 EC: 2.4.1.186; COMPND 7 ENGINEERED: YES; COMPND 8 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: GYG, GYG1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-R3-PRARE2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, KEYWDS 2 TRANSFERASE, GLYCOSYLTRANSFERASE, GLYCOGEN BIOSYNTHESIS, KEYWDS 3 GLYCOSYLATION EXPDTA X-RAY DIFFRACTION AUTHOR A.CHAIKUAD,D.S.FROESE,W.W.YUE,E.KRYSZTOFINSKA,F.VON DELFT,J.WEIGELT, AUTHOR 2 C.H.ARROWSMITH,A.M.EDWARDS,C.BOUNTRA,U.OPPERMANN,STRUCTURAL GENOMICS AUTHOR 3 CONSORTIUM (SGC) REVDAT 5 13-SEP-23 3RMV 1 REMARK SEQADV LINK REVDAT 4 11-JAN-12 3RMV 1 JRNL REVDAT 3 28-DEC-11 3RMV 1 JRNL REVDAT 2 14-DEC-11 3RMV 1 VERSN REVDAT 1 18-MAY-11 3RMV 0 JRNL AUTH A.CHAIKUAD,D.S.FROESE,G.BERRIDGE,F.VON DELFT,U.OPPERMANN, JRNL AUTH 2 W.W.YUE JRNL TITL CONFORMATIONAL PLASTICITY OF GLYCOGENIN AND ITS JRNL TITL 2 MALTOSACCHARIDE SUBSTRATE DURING GLYCOGEN BIOGENESIS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 108 21028 2011 JRNL REFN ISSN 0027-8424 JRNL PMID 22160680 JRNL DOI 10.1073/PNAS.1113921108 REMARK 2 REMARK 2 RESOLUTION. 1.82 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0110 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) : 1.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 24391 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 : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1309 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) : 1.82 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1779 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3930 REMARK 3 BIN FREE R VALUE SET COUNT : 93 REMARK 3 BIN FREE R VALUE : 0.3960 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1956 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 233 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.77000 REMARK 3 B22 (A**2) : -0.68000 REMARK 3 B33 (A**2) : 1.45000 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): 0.130 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.128 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.087 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.318 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2087 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1359 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2843 ; 1.456 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3334 ; 0.943 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 260 ; 6.407 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 87 ;36.157 ;24.368 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 335 ;13.174 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;11.829 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 329 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2277 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 416 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1267 ; 2.211 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 505 ; 0.651 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2063 ; 3.290 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 820 ; 4.783 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 774 ; 6.867 ;11.000 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): 2 ;11.650 ; 3.000 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 0 A 232 REMARK 3 ORIGIN FOR THE GROUP (A): 17.3752 15.3274 11.4722 REMARK 3 T TENSOR REMARK 3 T11: 0.0126 T22: 0.0260 REMARK 3 T33: 0.0179 T12: 0.0085 REMARK 3 T13: 0.0056 T23: -0.0204 REMARK 3 L TENSOR REMARK 3 L11: 2.2033 L22: 2.2428 REMARK 3 L33: 1.5755 L12: 0.1701 REMARK 3 L13: 0.5668 L23: -0.3164 REMARK 3 S TENSOR REMARK 3 S11: -0.0242 S12: -0.1238 S13: -0.0433 REMARK 3 S21: -0.0102 S22: 0.0461 S23: -0.0130 REMARK 3 S31: 0.0816 S32: -0.0249 S33: -0.0219 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 242 A 262 REMARK 3 ORIGIN FOR THE GROUP (A): 3.6927 8.4916 -0.1690 REMARK 3 T TENSOR REMARK 3 T11: 0.1278 T22: 0.1185 REMARK 3 T33: 0.0942 T12: -0.0770 REMARK 3 T13: -0.0236 T23: -0.0324 REMARK 3 L TENSOR REMARK 3 L11: 14.9127 L22: 14.0436 REMARK 3 L33: 15.7412 L12: -3.3772 REMARK 3 L13: 2.0945 L23: 3.8651 REMARK 3 S TENSOR REMARK 3 S11: 0.1326 S12: 0.0880 S13: -0.8263 REMARK 3 S21: 0.3038 S22: -0.1643 S23: 0.7391 REMARK 3 S31: 0.7291 S32: -0.8804 S33: 0.0317 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 3RMV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-APR-11. REMARK 100 THE DEPOSITION ID IS D_1000065127. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : FLAT GRAPHITE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25702 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.820 REMARK 200 RESOLUTION RANGE LOW (A) : 29.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.82 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.73900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3Q4S REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28% PEG SMEARS (PEG 2K, 3350, 4K, REMARK 280 5KMME), 0.05M MGSO4, 0.1M HEPES, PH 7.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 28.34000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.36000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.34000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.36000 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 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: 4570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 56.68000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 193 REMARK 465 ILE A 194 REMARK 465 TYR A 195 REMARK 465 SER A 196 REMARK 465 TYR A 197 REMARK 465 SER A 233 REMARK 465 GLU A 234 REMARK 465 ALA A 235 REMARK 465 HIS A 236 REMARK 465 ASP A 237 REMARK 465 PRO A 238 REMARK 465 ASN A 239 REMARK 465 MET A 240 REMARK 465 THR A 241 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 LEU A 198 CG CD1 CD2 REMARK 470 PHE A 201 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 202 CG CD CE NZ REMARK 470 HIS A 242 CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 261 CG CD1 CD2 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 MG MG A 267 O HOH A 473 1.58 REMARK 500 MG MG A 267 O HOH A 469 1.64 REMARK 500 O HOH A 472 O HOH A 473 2.18 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 104 CB - CG - OD1 ANGL. DEV. = 7.0 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 ASP A 104 32.99 -92.75 REMARK 500 ASP A 178 92.03 61.92 REMARK 500 ASN A 188 68.28 -161.20 REMARK 500 PRO A 243 10.58 -67.43 REMARK 500 LEU A 261 35.88 -77.14 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 MN A 263 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 102 OD2 REMARK 620 2 ASP A 104 OD1 97.0 REMARK 620 3 ASP A 104 OD2 152.5 55.6 REMARK 620 4 HIS A 212 NE2 96.7 92.9 88.0 REMARK 620 5 UDP A 264 O1A 90.8 85.2 85.0 172.5 REMARK 620 6 UDP A 264 O3B 104.2 156.7 102.4 94.1 84.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 267 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 155 OE2 REMARK 620 2 HOH A 469 O 77.4 REMARK 620 3 HOH A 472 O 173.6 97.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 267 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 155 OE2 REMARK 620 2 HOH A 472 O 98.3 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 263 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UDP A 264 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 265 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 266 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 267 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3QVB RELATED DB: PDB REMARK 900 HGYG1 (Y195F) WITH UDP,MN REMARK 900 RELATED ID: 3Q4S RELATED DB: PDB REMARK 900 HGYG1 (Y195F) APO FORM DBREF 3RMV A 1 262 UNP P46976 GLYG_HUMAN 1 262 SEQADV 3RMV SER A 0 UNP P46976 EXPRESSION TAG SEQADV 3RMV MET A 83 UNP P46976 THR 83 ENGINEERED MUTATION SEQRES 1 A 263 SER MET THR ASP GLN ALA PHE VAL THR LEU THR THR ASN SEQRES 2 A 263 ASP ALA TYR ALA LYS GLY ALA LEU VAL LEU GLY SER SER SEQRES 3 A 263 LEU LYS GLN HIS ARG THR THR ARG ARG LEU VAL VAL LEU SEQRES 4 A 263 ALA THR PRO GLN VAL SER ASP SER MET ARG LYS VAL LEU SEQRES 5 A 263 GLU THR VAL PHE ASP GLU VAL ILE MET VAL ASP VAL LEU SEQRES 6 A 263 ASP SER GLY ASP SER ALA HIS LEU THR LEU MET LYS ARG SEQRES 7 A 263 PRO GLU LEU GLY VAL MET LEU THR LYS LEU HIS CYS TRP SEQRES 8 A 263 SER LEU THR GLN TYR SER LYS CYS VAL PHE MET ASP ALA SEQRES 9 A 263 ASP THR LEU VAL LEU ALA ASN ILE ASP ASP LEU PHE ASP SEQRES 10 A 263 ARG GLU GLU LEU SER ALA ALA PRO ASP PRO GLY TRP PRO SEQRES 11 A 263 ASP CYS PHE ASN SER GLY VAL PHE VAL TYR GLN PRO SER SEQRES 12 A 263 VAL GLU THR TYR ASN GLN LEU LEU HIS LEU ALA SER GLU SEQRES 13 A 263 GLN GLY SER PHE ASP GLY GLY ASP GLN GLY ILE LEU ASN SEQRES 14 A 263 THR PHE PHE SER SER TRP ALA THR THR ASP ILE ARG LYS SEQRES 15 A 263 HIS LEU PRO PHE ILE TYR ASN LEU SER SER ILE SER ILE SEQRES 16 A 263 TYR SER TYR LEU PRO ALA PHE LYS VAL PHE GLY ALA SER SEQRES 17 A 263 ALA LYS VAL VAL HIS PHE LEU GLY ARG VAL LYS PRO TRP SEQRES 18 A 263 ASN TYR THR TYR ASP PRO LYS THR LYS SER VAL LYS SER SEQRES 19 A 263 GLU ALA HIS ASP PRO ASN MET THR HIS PRO GLU PHE LEU SEQRES 20 A 263 ILE LEU TRP TRP ASN ILE PHE THR THR ASN VAL LEU PRO SEQRES 21 A 263 LEU LEU GLN HET MN A 263 1 HET UDP A 264 25 HET EDO A 265 4 HET EDO A 266 4 HET MG A 267 2 HETNAM MN MANGANESE (II) ION HETNAM UDP URIDINE-5'-DIPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETNAM MG MAGNESIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 MN MN 2+ FORMUL 3 UDP C9 H14 N2 O12 P2 FORMUL 4 EDO 2(C2 H6 O2) FORMUL 6 MG MG 2+ FORMUL 7 HOH *233(H2 O) HELIX 1 1 ASN A 12 HIS A 29 1 18 HELIX 2 2 SER A 44 PHE A 55 1 12 HELIX 3 3 ALA A 70 ARG A 77 1 8 HELIX 4 4 LEU A 80 HIS A 88 1 9 HELIX 5 5 CYS A 89 LEU A 92 5 4 HELIX 6 6 ILE A 111 ARG A 117 5 7 HELIX 7 7 SER A 142 GLY A 157 1 16 HELIX 8 8 ASP A 163 PHE A 171 1 9 HELIX 9 9 ASP A 178 HIS A 182 5 5 HELIX 10 10 PRO A 184 ASN A 188 5 5 HELIX 11 11 LEU A 198 GLY A 205 1 8 HELIX 12 12 ALA A 206 ALA A 208 5 3 HELIX 13 13 LYS A 218 TYR A 222 5 5 HELIX 14 14 PRO A 243 ASN A 256 1 14 HELIX 15 15 VAL A 257 GLN A 262 5 6 SHEET 1 A 6 GLU A 57 MET A 60 0 SHEET 2 A 6 ARG A 33 ALA A 39 1 N VAL A 37 O ILE A 59 SHEET 3 A 6 MET A 1 THR A 10 1 N PHE A 6 O VAL A 36 SHEET 4 A 6 LYS A 97 MET A 101 1 O MET A 101 N VAL A 7 SHEET 5 A 6 PHE A 132 TYR A 139 -1 O TYR A 139 N CYS A 98 SHEET 6 A 6 SER A 121 PRO A 124 -1 N SER A 121 O VAL A 138 SHEET 1 B 2 THR A 105 VAL A 107 0 SHEET 2 B 2 VAL A 210 HIS A 212 -1 O VAL A 211 N LEU A 106 SHEET 1 C 2 TYR A 224 ASP A 225 0 SHEET 2 C 2 SER A 230 VAL A 231 -1 O SER A 230 N ASP A 225 LINK OD2 ASP A 102 MN MN A 263 1555 1555 1.98 LINK OD1 ASP A 104 MN MN A 263 1555 1555 2.02 LINK OD2 ASP A 104 MN MN A 263 1555 1555 2.46 LINK OE2BGLU A 155 MG B MG A 267 1555 1555 1.92 LINK OE2AGLU A 155 MG A MG A 267 1555 1555 1.95 LINK NE2 HIS A 212 MN MN A 263 1555 1555 2.12 LINK MN MN A 263 O1A UDP A 264 1555 1555 1.98 LINK MN MN A 263 O3B UDP A 264 1555 1555 2.01 LINK MG B MG A 267 O HOH A 469 1555 1555 2.74 LINK MG B MG A 267 O HOH A 472 1555 1555 1.82 LINK MG A MG A 267 O HOH A 472 1555 1555 2.27 CISPEP 1 GLU A 119 LEU A 120 0 -6.64 SITE 1 AC1 4 ASP A 102 ASP A 104 HIS A 212 UDP A 264 SITE 1 AC2 16 LEU A 9 THR A 10 THR A 11 ASN A 12 SITE 2 AC2 16 TYR A 15 ASP A 102 ALA A 103 ASP A 104 SITE 3 AC2 16 HIS A 212 GLY A 215 LYS A 218 MN A 263 SITE 4 AC2 16 HOH A 424 HOH A 426 HOH A 451 HOH A 482 SITE 1 AC3 8 GLU A 119 LEU A 120 PHE A 171 SER A 173 SITE 2 AC3 8 TRP A 174 LYS A 181 HOH A 268 HOH A 311 SITE 1 AC4 3 ASP A 178 ILE A 179 HOH A 483 SITE 1 AC5 7 ASP A 3 GLN A 94 HIS A 151 GLU A 155 SITE 2 AC5 7 HOH A 469 HOH A 472 HOH A 473 CRYST1 56.680 100.720 48.720 90.00 90.00 90.00 P 21 21 2 4 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 0.017643 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009929 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020525 0.00000