HEADER TRANSFERASE 25-FEB-11 3QVB
TITLE CRYSTAL STRUCTURE OF HUMAN GLYCOGENIN-1 (GYG1) COMPLEXED WITH
TITLE 2 MANGANESE AND UDP
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: GLYCOGENIN-1;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: GLYCOGENIN (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 3QVB 1 REMARK SEQADV LINK
REVDAT 4 11-JAN-12 3QVB 1 JRNL
REVDAT 3 28-DEC-11 3QVB 1 JRNL
REVDAT 2 14-DEC-11 3QVB 1 VERSN
REVDAT 1 23-MAR-11 3QVB 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. 2.26 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) : 2.26
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.03
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 3 NUMBER OF REFLECTIONS : 13168
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) : 0.202
REMARK 3 R VALUE (WORKING SET) : 0.199
REMARK 3 FREE R VALUE : 0.256
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 693
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) : 2.26
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.32
REMARK 3 REFLECTION IN BIN (WORKING SET) : 946
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.53
REMARK 3 BIN R VALUE (WORKING SET) : 0.3060
REMARK 3 BIN FREE R VALUE SET COUNT : 56
REMARK 3 BIN FREE R VALUE : 0.3070
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1972
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 46
REMARK 3 SOLVENT ATOMS : 136
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 38.70
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.93
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.39000
REMARK 3 B22 (A**2) : -1.23000
REMARK 3 B33 (A**2) : 1.61000
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): NULL
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.239
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.170
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.310
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2080 ; 0.016 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): 1365 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2826 ; 1.487 ; 1.969
REMARK 3 BOND ANGLES OTHERS (DEGREES): 3340 ; 0.991 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 252 ; 6.450 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 87 ;37.429 ;24.483
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 330 ;13.704 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;22.815 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 326 ; 0.087 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2247 ; 0.005 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 412 ; 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): 1258 ; 0.746 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 503 ; 0.150 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2042 ; 1.402 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 822 ; 2.194 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 782 ; 3.445 ; 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 : 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 231
REMARK 3 ORIGIN FOR THE GROUP (A): 17.7050 15.3700 11.6080
REMARK 3 T TENSOR
REMARK 3 T11: 0.0492 T22: 0.0282
REMARK 3 T33: 0.0782 T12: 0.0179
REMARK 3 T13: 0.0274 T23: -0.0323
REMARK 3 L TENSOR
REMARK 3 L11: 1.4858 L22: 1.6531
REMARK 3 L33: 0.8631 L12: -0.0181
REMARK 3 L13: 0.4937 L23: -0.2820
REMARK 3 S TENSOR
REMARK 3 S11: -0.0098 S12: -0.1035 S13: -0.0492
REMARK 3 S21: 0.0109 S22: 0.0409 S23: 0.0279
REMARK 3 S31: -0.0024 S32: -0.0457 S33: -0.0310
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 232 A 262
REMARK 3 ORIGIN FOR THE GROUP (A): 3.9900 8.5990 -1.1910
REMARK 3 T TENSOR
REMARK 3 T11: 0.2481 T22: 0.1295
REMARK 3 T33: 0.0607 T12: -0.1204
REMARK 3 T13: -0.0756 T23: -0.0180
REMARK 3 L TENSOR
REMARK 3 L11: 10.1656 L22: 12.2057
REMARK 3 L33: 11.6414 L12: -4.8141
REMARK 3 L13: 2.1290 L23: 3.5360
REMARK 3 S TENSOR
REMARK 3 S11: 0.0029 S12: -0.0664 S13: -0.7227
REMARK 3 S21: -1.5372 S22: 0.2017 S23: 0.5087
REMARK 3 S31: 0.2854 S32: -0.9196 S33: -0.2046
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 3QVB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-MAR-11.
REMARK 100 THE DEPOSITION ID IS D_1000064148.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 22-JAN-11
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : 8.5
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 : 13862
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.260
REMARK 200 RESOLUTION RANGE LOW (A) : 29.970
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 200 DATA REDUNDANCY : 3.900
REMARK 200 R MERGE (I) : 0.09300
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.7000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.26
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1
REMARK 200 DATA REDUNDANCY IN SHELL : 3.90
REMARK 200 R MERGE FOR SHELL (I) : 0.60500
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 (%): 48.66
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, 0.2M AMMONIUM SULFATE,
REMARK 280 0.1M TRIS, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE
REMARK 280 293.15K
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 28.70000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.48500
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.70000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.48500
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: 5030 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 21850 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 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 57.40000
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 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 HOH A 405 LIES ON A SPECIAL POSITION.
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 PHE A 195
REMARK 465 SER A 196
REMARK 465 TYR A 197
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 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 ILE A 192 CG1 CG2 CD1
REMARK 470 ARG A 216 CG CD NE CZ NH1 NH2
REMARK 470 THR A 241 OG1 CG2
REMARK 470 HIS A 242 CG ND1 CD2 CE1 NE2
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. = 8.3 DEGREES
REMARK 500 ASP A 104 CB - CG - OD2 ANGL. DEV. = -5.9 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 171 55.51 -97.01
REMARK 500 ASP A 178 93.68 54.56
REMARK 500 ASN A 188 67.66 -166.44
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 MN A 263 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 102 OD2
REMARK 620 2 ASP A 104 OD1 105.7
REMARK 620 3 HIS A 212 NE2 102.2 87.6
REMARK 620 4 UDP A 264 O2B 108.1 144.2 96.3
REMARK 620 5 UDP A 264 O1A 93.1 85.5 164.4 81.4
REMARK 620 N 1 2 3 4
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 EDO A 267
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 268
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 269
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3Q4S RELATED DB: PDB
REMARK 900 APO FORM
DBREF 3QVB A 1 262 UNP P46976 GLYG_HUMAN 1 262
SEQADV 3QVB SER A 0 UNP P46976 EXPRESSION TAG
SEQADV 3QVB PHE A 195 UNP P46976 TYR 195 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 THR 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 PHE 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 EDO A 267 4
HET EDO A 268 4
HET EDO A 269 4
HETNAM MN MANGANESE (II) ION
HETNAM UDP URIDINE-5'-DIPHOSPHATE
HETNAM EDO 1,2-ETHANEDIOL
HETSYN EDO ETHYLENE GLYCOL
FORMUL 2 MN MN 2+
FORMUL 3 UDP C9 H14 N2 O12 P2
FORMUL 4 EDO 5(C2 H6 O2)
FORMUL 9 HOH *136(H2 O)
HELIX 1 1 ASN A 12 HIS A 29 1 18
HELIX 2 2 SER A 44 GLU A 52 1 9
HELIX 3 3 ALA A 70 ARG A 77 1 8
HELIX 4 4 LEU A 80 LEU A 87 1 8
HELIX 5 5 HIS A 88 LEU A 92 5 5
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 GLY A 162 PHE A 171 1 10
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 VAL A 257 1 15
SHEET 1 A 6 GLU A 57 MET A 60 0
SHEET 2 A 6 ARG A 33 ALA A 39 1 N ALA A 39 O ILE A 59
SHEET 3 A 6 MET A 1 THR A 10 1 N THR A 8 O LEU A 38
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 PHE A 137 N PHE A 100
SHEET 6 A 6 SER A 121 PRO A 124 -1 N SER A 121 O VAL A 138
SHEET 1 B 3 THR A 105 VAL A 107 0
SHEET 2 B 3 VAL A 210 HIS A 212 -1 O VAL A 211 N LEU A 106
SHEET 3 B 3 LEU A 189 SER A 190 1 N LEU A 189 O VAL A 210
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 1.97
LINK OD1 ASP A 104 MN MN A 263 1555 1555 2.04
LINK NE2 HIS A 212 MN MN A 263 1555 1555 2.10
LINK MN MN A 263 O2B UDP A 264 1555 1555 1.94
LINK MN MN A 263 O1A UDP A 264 1555 1555 2.28
CISPEP 1 GLU A 119 LEU A 120 0 -8.54
SITE 1 AC1 4 ASP A 102 ASP A 104 HIS A 212 UDP A 264
SITE 1 AC2 14 LEU A 9 THR A 10 THR A 11 TYR A 15
SITE 2 AC2 14 VAL A 82 ASP A 102 ALA A 103 ASP A 104
SITE 3 AC2 14 HIS A 212 LEU A 214 GLY A 215 LYS A 218
SITE 4 AC2 14 MN A 263 HOH A 388
SITE 1 AC3 3 HIS A 29 ARG A 30 ASN A 110
SITE 1 AC4 4 THR A 93 SER A 142 VAL A 143 GLU A 144
SITE 1 AC5 5 GLU A 119 LEU A 120 SER A 173 LYS A 181
SITE 2 AC5 5 HOH A 364
SITE 1 AC6 3 HIS A 88 LEU A 92 HOH A 308
SITE 1 AC7 7 SER A 44 ASP A 45 SER A 46 SER A 158
SITE 2 AC7 7 PHE A 159 ASP A 160 GLY A 161
CRYST1 57.400 100.970 48.940 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 0.017422 0.000000 0.000000 0.00000
SCALE2 0.000000 0.009904 0.000000 0.00000
SCALE3 0.000000 0.000000 0.020433 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
