PDB Short entry for 5IKO HEADER TRANSFERASE 03-MAR-16 5IKO TITLE CRYSTAL STRUCTURE OF HUMAN BRAIN GLYCOGEN PHOSPHORYLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCOGEN PHOSPHORYLASE, BRAIN FORM; COMPND 3 CHAIN: A; COMPND 4 EC: 2.4.1.1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 TISSUE: BRAIN ISOFORM; SOURCE 6 GENE: PYGB; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GP, GLYCOGEN PHOSPHORYLASE, GLYCOGEN METABOLISM, GLYCOGEN DISEASE, KEYWDS 2 GLYCOSYLTRANSFERASE, NUCLEOTIDE-BINDING, ALLOSTERIC ENZYME, KEYWDS 3 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.MATHIEU,I.LI DE LA SIERRA-GALLAY,X.XU,A.HAOUZ,F.RODRIGUES-LIMA REVDAT 4 10-JAN-24 5IKO 1 REMARK REVDAT 3 16-OCT-19 5IKO 1 REMARK REVDAT 2 07-SEP-16 5IKO 1 JRNL REVDAT 1 20-JUL-16 5IKO 0 JRNL AUTH C.MATHIEU,I.L.DE LA SIERRA-GALLAY,R.DUVAL,X.XU,A.COCAIGN, JRNL AUTH 2 T.LEGER,G.WOFFENDIN,J.M.CAMADRO,C.ETCHEBEST,A.HAOUZ, JRNL AUTH 3 J.M.DUPRET,F.RODRIGUES-LIMA JRNL TITL INSIGHTS INTO BRAIN GLYCOGEN METABOLISM: THE STRUCTURE OF JRNL TITL 2 HUMAN BRAIN GLYCOGEN PHOSPHORYLASE. JRNL REF J.BIOL.CHEM. V. 291 18072 2016 JRNL REFN ESSN 1083-351X JRNL PMID 27402852 JRNL DOI 10.1074/JBC.M116.738898 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.37 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 35450 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1866 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2499 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.73 REMARK 3 BIN R VALUE (WORKING SET) : 0.2890 REMARK 3 BIN FREE R VALUE SET COUNT : 131 REMARK 3 BIN FREE R VALUE : 0.3810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6524 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 63 REMARK 3 SOLVENT ATOMS : 84 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.33 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.60000 REMARK 3 B22 (A**2) : 0.60000 REMARK 3 B33 (A**2) : -1.93000 REMARK 3 B12 (A**2) : 0.30000 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): 0.415 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.264 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.213 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.873 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6743 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6458 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9119 ; 1.687 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14842 ; 1.087 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 805 ; 4.569 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 332 ;38.371 ;23.916 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1166 ;18.259 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 48 ;17.525 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 986 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7548 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1579 ; 0.002 ; 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): 3226 ; 5.165 ; 6.587 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3225 ; 5.164 ; 6.586 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4026 ; 7.053 ; 9.886 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4027 ; 7.053 ; 9.888 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3515 ; 6.093 ; 7.179 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3515 ; 6.092 ; 7.179 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5093 ; 8.687 ;10.533 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 28583 ;11.361 ;63.084 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 28573 ;11.362 ;63.086 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 5IKO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000218943. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.980110 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37317 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 47.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 26.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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: 1Z8D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28 % (V/V) PEG 400, 0.2 M CALCIUM REMARK 280 CHLORIDE, AND 0.1 M HEPES, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 6 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z REMARK 290 6555 X-Y,X,Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 21180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 115310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -74.0 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 85.83000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 445.98576 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 257.49000 REMARK 350 BIOMT2 3 -0.866025 0.500000 0.000000 148.66192 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 245.84000 REMARK 350 BIOMT1 4 0.500000 0.866025 0.000000 -171.66000 REMARK 350 BIOMT2 4 0.866025 -0.500000 0.000000 297.32384 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 245.84000 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 GLY A -3 REMARK 465 SER A -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 REMARK 465 ALA A 1 REMARK 465 LYS A 2 REMARK 465 PRO A 3 REMARK 465 LEU A 4 REMARK 465 THR A 5 REMARK 465 ASP A 6 REMARK 465 SER A 7 REMARK 465 GLU A 8 REMARK 465 LYS A 9 REMARK 465 ARG A 10 REMARK 465 LYS A 11 REMARK 465 GLN A 12 REMARK 465 ILE A 13 REMARK 465 SER A 14 REMARK 465 VAL A 15 REMARK 465 ARG A 16 REMARK 465 GLY A 17 REMARK 465 LEU A 18 REMARK 465 ALA A 19 REMARK 465 GLY A 20 REMARK 465 PHE A 252 REMARK 465 LYS A 253 REMARK 465 LEU A 254 REMARK 465 GLN A 255 REMARK 465 ASN A 284 REMARK 465 PHE A 285 REMARK 465 CYS A 318 REMARK 465 ARG A 319 REMARK 465 ASP A 320 REMARK 465 PRO A 321 REMARK 465 VAL A 322 REMARK 465 ARG A 323 REMARK 465 PRO A 840 REMARK 465 ARG A 841 REMARK 465 ASP A 842 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 43 NE - CZ - NH2 ANGL. DEV. = -3.6 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 78 60.97 27.70 REMARK 500 ASN A 133 -53.78 -135.10 REMARK 500 ILE A 165 -65.11 -107.73 REMARK 500 PHE A 166 147.50 175.56 REMARK 500 TYR A 203 -132.95 67.58 REMARK 500 TYR A 280 61.87 38.97 REMARK 500 GLU A 287 38.41 -84.76 REMARK 500 PHE A 316 89.40 66.02 REMARK 500 ASP A 339 -177.02 73.45 REMARK 500 LEU A 380 135.61 64.73 REMARK 500 LEU A 492 -70.34 -144.73 REMARK 500 SER A 674 -92.14 -138.60 REMARK 500 SER A 751 58.31 -141.16 REMARK 500 ILE A 824 -55.48 -124.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue P6G A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue P6G A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PLP A 905 DBREF 5IKO A 0 842 UNP P11216 PYGB_HUMAN 1 843 SEQADV 5IKO GLY A -3 UNP P11216 EXPRESSION TAG SEQADV 5IKO SER A -2 UNP P11216 EXPRESSION TAG SEQADV 5IKO HIS A -1 UNP P11216 EXPRESSION TAG SEQRES 1 A 846 GLY SER HIS MET ALA LYS PRO LEU THR ASP SER GLU LYS SEQRES 2 A 846 ARG LYS GLN ILE SER VAL ARG GLY LEU ALA GLY LEU GLY SEQRES 3 A 846 ASP VAL ALA GLU VAL ARG LYS SER PHE ASN ARG HIS LEU SEQRES 4 A 846 HIS PHE THR LEU VAL LYS ASP ARG ASN VAL ALA THR PRO SEQRES 5 A 846 ARG ASP TYR PHE PHE ALA LEU ALA HIS THR VAL ARG ASP SEQRES 6 A 846 HIS LEU VAL GLY ARG TRP ILE ARG THR GLN GLN HIS TYR SEQRES 7 A 846 TYR GLU ARG ASP PRO LYS ARG ILE TYR TYR LEU SER LEU SEQRES 8 A 846 GLU PHE TYR MET GLY ARG THR LEU GLN ASN THR MET VAL SEQRES 9 A 846 ASN LEU GLY LEU GLN ASN ALA CYS ASP GLU ALA ILE TYR SEQRES 10 A 846 GLN LEU GLY LEU ASP LEU GLU GLU LEU GLU GLU ILE GLU SEQRES 11 A 846 GLU ASP ALA GLY LEU GLY ASN GLY GLY LEU GLY ARG LEU SEQRES 12 A 846 ALA ALA CYS PHE LEU ASP SER MET ALA THR LEU GLY LEU SEQRES 13 A 846 ALA ALA TYR GLY TYR GLY ILE ARG TYR GLU PHE GLY ILE SEQRES 14 A 846 PHE ASN GLN LYS ILE VAL ASN GLY TRP GLN VAL GLU GLU SEQRES 15 A 846 ALA ASP ASP TRP LEU ARG TYR GLY ASN PRO TRP GLU LYS SEQRES 16 A 846 ALA ARG PRO GLU TYR MET LEU PRO VAL HIS PHE TYR GLY SEQRES 17 A 846 ARG VAL GLU HIS THR PRO ASP GLY VAL LYS TRP LEU ASP SEQRES 18 A 846 THR GLN VAL VAL LEU ALA MET PRO TYR ASP THR PRO VAL SEQRES 19 A 846 PRO GLY TYR LYS ASN ASN THR VAL ASN THR MET ARG LEU SEQRES 20 A 846 TRP SER ALA LYS ALA PRO ASN ASP PHE LYS LEU GLN ASP SEQRES 21 A 846 PHE ASN VAL GLY ASP TYR ILE GLU ALA VAL LEU ASP ARG SEQRES 22 A 846 ASN LEU ALA GLU ASN ILE SER ARG VAL LEU TYR PRO ASN SEQRES 23 A 846 ASP ASN PHE PHE GLU GLY LYS GLU LEU ARG LEU LYS GLN SEQRES 24 A 846 GLU TYR PHE VAL VAL ALA ALA THR LEU GLN ASP ILE ILE SEQRES 25 A 846 ARG ARG PHE LYS SER SER LYS PHE GLY CYS ARG ASP PRO SEQRES 26 A 846 VAL ARG THR CYS PHE GLU THR PHE PRO ASP LYS VAL ALA SEQRES 27 A 846 ILE GLN LEU ASN ASP THR HIS PRO ALA LEU SER ILE PRO SEQRES 28 A 846 GLU LEU MET ARG ILE LEU VAL ASP VAL GLU LYS VAL ASP SEQRES 29 A 846 TRP ASP LYS ALA TRP GLU ILE THR LYS LYS THR CYS ALA SEQRES 30 A 846 TYR THR ASN HIS THR VAL LEU PRO GLU ALA LEU GLU ARG SEQRES 31 A 846 TRP PRO VAL SER MET PHE GLU LYS LEU LEU PRO ARG HIS SEQRES 32 A 846 LEU GLU ILE ILE TYR ALA ILE ASN GLN ARG HIS LEU ASP SEQRES 33 A 846 HIS VAL ALA ALA LEU PHE PRO GLY ASP VAL ASP ARG LEU SEQRES 34 A 846 ARG ARG MET SER VAL ILE GLU GLU GLY ASP CYS LYS ARG SEQRES 35 A 846 ILE ASN MET ALA HIS LEU CYS VAL ILE GLY SER HIS ALA SEQRES 36 A 846 VAL ASN GLY VAL ALA ARG ILE HIS SER GLU ILE VAL LYS SEQRES 37 A 846 GLN SER VAL PHE LYS ASP PHE TYR GLU LEU GLU PRO GLU SEQRES 38 A 846 LYS PHE GLN ASN LYS THR ASN GLY ILE THR PRO ARG ARG SEQRES 39 A 846 TRP LEU LEU LEU CYS ASN PRO GLY LEU ALA ASP THR ILE SEQRES 40 A 846 VAL GLU LYS ILE GLY GLU GLU PHE LEU THR ASP LEU SER SEQRES 41 A 846 GLN LEU LYS LYS LEU LEU PRO LEU VAL SER ASP GLU VAL SEQRES 42 A 846 PHE ILE ARG ASP VAL ALA LYS VAL LYS GLN GLU ASN LYS SEQRES 43 A 846 LEU LYS PHE SER ALA PHE LEU GLU LYS GLU TYR LYS VAL SEQRES 44 A 846 LYS ILE ASN PRO SER SER MET PHE ASP VAL HIS VAL LYS SEQRES 45 A 846 ARG ILE HIS GLU TYR LYS ARG GLN LEU LEU ASN CYS LEU SEQRES 46 A 846 HIS VAL VAL THR LEU TYR ASN ARG ILE LYS ARG ASP PRO SEQRES 47 A 846 ALA LYS ALA PHE VAL PRO ARG THR VAL MET ILE GLY GLY SEQRES 48 A 846 LYS ALA ALA PRO GLY TYR HIS MET ALA LYS LEU ILE ILE SEQRES 49 A 846 LYS LEU VAL THR SER ILE GLY ASP VAL VAL ASN HIS ASP SEQRES 50 A 846 PRO VAL VAL GLY ASP ARG LEU LYS VAL ILE PHE LEU GLU SEQRES 51 A 846 ASN TYR ARG VAL SER LEU ALA GLU LYS VAL ILE PRO ALA SEQRES 52 A 846 ALA ASP LEU SER GLN GLN ILE SER THR ALA GLY THR GLU SEQRES 53 A 846 ALA SER GLY THR GLY ASN MET LYS PHE MET LEU ASN GLY SEQRES 54 A 846 ALA LEU THR ILE GLY THR MET ASP GLY ALA ASN VAL GLU SEQRES 55 A 846 MET ALA GLU GLU ALA GLY ALA GLU ASN LEU PHE ILE PHE SEQRES 56 A 846 GLY LEU ARG VAL GLU ASP VAL GLU ALA LEU ASP ARG LYS SEQRES 57 A 846 GLY TYR ASN ALA ARG GLU TYR TYR ASP HIS LEU PRO GLU SEQRES 58 A 846 LEU LYS GLN ALA VAL ASP GLN ILE SER SER GLY PHE PHE SEQRES 59 A 846 SER PRO LYS GLU PRO ASP CYS PHE LYS ASP ILE VAL ASN SEQRES 60 A 846 MET LEU MET HIS HIS ASP ARG PHE LYS VAL PHE ALA ASP SEQRES 61 A 846 TYR GLU ALA TYR MET GLN CYS GLN ALA GLN VAL ASP GLN SEQRES 62 A 846 LEU TYR ARG ASN PRO LYS GLU TRP THR LYS LYS VAL ILE SEQRES 63 A 846 ARG ASN ILE ALA CYS SER GLY LYS PHE SER SER ASP ARG SEQRES 64 A 846 THR ILE THR GLU TYR ALA ARG GLU ILE TRP GLY VAL GLU SEQRES 65 A 846 PRO SER ASP LEU GLN ILE PRO PRO PRO ASN ILE PRO ARG SEQRES 66 A 846 ASP HET P6G A 901 19 HET P6G A 902 19 HET PO4 A 903 5 HET PO4 A 904 5 HET PLP A 905 15 HETNAM P6G HEXAETHYLENE GLYCOL HETNAM PO4 PHOSPHATE ION HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETSYN P6G POLYETHYLENE GLYCOL PEG400 HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 2 P6G 2(C12 H26 O7) FORMUL 4 PO4 2(O4 P 3-) FORMUL 6 PLP C8 H10 N O6 P FORMUL 7 HOH *84(H2 O) HELIX 1 AA1 LEU A 21 THR A 38 1 18 HELIX 2 AA2 THR A 47 ASP A 78 1 32 HELIX 3 AA3 THR A 94 LEU A 102 1 9 HELIX 4 AA4 LEU A 104 LEU A 115 1 12 HELIX 5 AA5 ASP A 118 GLU A 126 1 9 HELIX 6 AA6 GLY A 134 LEU A 150 1 17 HELIX 7 AA7 PRO A 194 MET A 197 5 4 HELIX 8 AA8 ASN A 258 ASN A 274 1 17 HELIX 9 AA9 ILE A 275 ARG A 277 5 3 HELIX 10 AB1 GLY A 288 SER A 313 1 26 HELIX 11 AB2 THR A 324 GLU A 327 5 4 HELIX 12 AB3 THR A 328 LYS A 332 1 5 HELIX 13 AB4 THR A 340 ALA A 343 5 4 HELIX 14 AB5 LEU A 344 VAL A 356 1 13 HELIX 15 AB6 ASP A 360 THR A 371 1 12 HELIX 16 AB7 LEU A 380 LEU A 384 5 5 HELIX 17 AB8 VAL A 389 LEU A 396 1 8 HELIX 18 AB9 LEU A 396 PHE A 418 1 23 HELIX 19 AC1 ASP A 421 SER A 429 1 9 HELIX 20 AC2 MET A 441 GLY A 448 1 8 HELIX 21 AC3 ALA A 456 SER A 466 1 11 HELIX 22 AC4 PHE A 468 GLU A 475 1 8 HELIX 23 AC5 ASN A 496 GLY A 508 1 13 HELIX 24 AC6 GLU A 509 THR A 513 5 5 HELIX 25 AC7 ASP A 514 SER A 526 5 13 HELIX 26 AC8 ASP A 527 LYS A 554 1 28 HELIX 27 AC9 ARG A 575 ASP A 593 1 19 HELIX 28 AD1 TYR A 613 HIS A 632 1 20 HELIX 29 AD2 VAL A 636 ASP A 638 5 3 HELIX 30 AD3 ARG A 649 ILE A 657 1 9 HELIX 31 AD4 THR A 676 ASN A 684 1 9 HELIX 32 AD5 GLY A 694 GLY A 704 1 11 HELIX 33 AD6 ALA A 705 LEU A 708 5 4 HELIX 34 AD7 ARG A 714 GLY A 725 1 12 HELIX 35 AD8 ALA A 728 HIS A 734 1 7 HELIX 36 AD9 LEU A 735 GLY A 748 1 14 HELIX 37 AE1 PHE A 758 HIS A 768 1 11 HELIX 38 AE2 LYS A 772 ARG A 792 1 21 HELIX 39 AE3 ASN A 793 CYS A 807 1 15 HELIX 40 AE4 SER A 808 PHE A 811 5 4 HELIX 41 AE5 SER A 812 ILE A 824 1 13 SHEET 1 AA1 3 LYS A 191 ALA A 192 0 SHEET 2 AA1 3 GLY A 212 PRO A 231 -1 O ASP A 227 N LYS A 191 SHEET 3 AA1 3 LEU A 198 THR A 209 -1 N VAL A 200 O VAL A 221 SHEET 1 AA2 9 LYS A 191 ALA A 192 0 SHEET 2 AA2 9 GLY A 212 PRO A 231 -1 O ASP A 227 N LYS A 191 SHEET 3 AA2 9 VAL A 238 LYS A 247 -1 O LYS A 247 N LEU A 222 SHEET 4 AA2 9 ALA A 154 ILE A 159 1 N GLY A 156 O ARG A 242 SHEET 5 AA2 9 ARG A 81 LEU A 85 1 N ILE A 82 O TYR A 155 SHEET 6 AA2 9 VAL A 333 ASN A 338 1 O GLN A 336 N TYR A 83 SHEET 7 AA2 9 CYS A 372 THR A 375 1 O THR A 375 N LEU A 337 SHEET 8 AA2 9 VAL A 452 GLY A 454 1 O ASN A 453 N TYR A 374 SHEET 9 AA2 9 PHE A 479 ASN A 481 1 O GLN A 480 N VAL A 452 SHEET 1 AA3 2 ASN A 167 VAL A 171 0 SHEET 2 AA3 2 TRP A 174 GLU A 178 -1 O VAL A 176 N LYS A 169 SHEET 1 AA4 3 ARG A 386 PRO A 388 0 SHEET 2 AA4 3 ARG A 438 ASN A 440 -1 O ILE A 439 N TRP A 387 SHEET 3 AA4 3 ILE A 431 GLU A 432 -1 N GLU A 432 O ARG A 438 SHEET 1 AA5 6 LEU A 640 LEU A 645 0 SHEET 2 AA5 6 ARG A 601 GLY A 606 1 N VAL A 603 O LYS A 641 SHEET 3 AA5 6 MET A 562 VAL A 567 1 N ASP A 564 O MET A 604 SHEET 4 AA5 6 LEU A 662 GLN A 665 1 O LEU A 662 N PHE A 563 SHEET 5 AA5 6 LEU A 687 GLY A 690 1 O LEU A 687 N SER A 663 SHEET 6 AA5 6 PHE A 709 ILE A 710 1 O PHE A 709 N THR A 688 LINK NZ LYS A 680 C4A PLP A 905 1555 1555 1.45 SITE 1 AC1 3 ALA A 720 LYS A 724 TYR A 731 SITE 1 AC2 9 VAL A 40 ASP A 42 VAL A 45 TRP A 67 SITE 2 AC2 9 ILE A 68 GLN A 71 ARG A 193 TYR A 196 SITE 3 AC2 9 ASP A 227 SITE 1 AC3 3 HIS A 208 ARG A 398 PO4 A 904 SITE 1 AC4 3 TRP A 361 ARG A 409 PO4 A 903 SITE 1 AC5 10 TYR A 90 TRP A 491 LYS A 568 ARG A 649 SITE 2 AC5 10 VAL A 650 GLY A 675 THR A 676 GLY A 677 SITE 3 AC5 10 ASN A 678 LYS A 680 CRYST1 171.660 171.660 122.920 90.00 90.00 120.00 P 6 2 2 12 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 0.005825 0.003363 0.000000 0.00000 SCALE2 0.000000 0.006727 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008135 0.00000