PDB Short entry for 2GJ4 HEADER TRANSFERASE 30-MAR-06 2GJ4 TITLE STRUCTURE OF RABBIT MUSCLE GLYCOGEN PHOSPHORYLASE IN COMPLEX WITH TITLE 2 LIGAND COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCOGEN PHOSPHORYLASE, MUSCLE FORM; COMPND 3 CHAIN: A; COMPND 4 EC: 2.4.1.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYCTOLAGUS CUNICULUS; SOURCE 3 ORGANISM_COMMON: RABBIT; SOURCE 4 ORGANISM_TAXID: 9986; SOURCE 5 OTHER_DETAILS: MUSCLE TISSUE KEYWDS GLYCOGEN PHOSPHORYLASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR L.R.OTTERBEIN,A.D.PANNIFER,J.TUCKER,J.BREED,N.G.OIKONOMAKOS, AUTHOR 2 S.ROWSELL,R.A.PAUPTIT,M.CLAIRE REVDAT 3 13-JUL-11 2GJ4 1 VERSN REVDAT 2 24-FEB-09 2GJ4 1 VERSN REVDAT 1 13-FEB-07 2GJ4 0 JRNL AUTH P.R.WHITTAMORE,M.S.ADDIE,S.N.BENNETT,A.M.BIRCH,M.BUTTERS, JRNL AUTH 2 L.GODFREY,P.W.KENNY,A.D.MORLEY,P.M.MURRAY,N.G.OIKONOMAKOS, JRNL AUTH 3 L.R.OTTERBEIN,A.D.PANNIFER,J.S.PARKER,K.READMAN, JRNL AUTH 4 P.S.SIEDLECKI,P.SCHOFIELD,A.STOCKER,M.J.TAYLOR,L.A.TOWNSEND, JRNL AUTH 5 D.P.WHALLEY,J.WHITEHOUSE JRNL TITL NOVEL THIENOPYRROLE GLYCOGEN PHOSPHORYLASE INHIBITORS: JRNL TITL 2 SYNTHESIS, IN VITRO SAR AND CRYSTALLOGRAPHIC STUDIES. JRNL REF BIOORG.MED.CHEM.LETT. V. 16 5567 2006 JRNL REFN ISSN 0960-894X JRNL PMID 16945526 JRNL DOI 10.1016/J.BMCL.2006.08.047 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 71.8 REMARK 3 NUMBER OF REFLECTIONS : 86732 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 : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4629 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1007 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 11.44 REMARK 3 BIN R VALUE (WORKING SET) : 0.3020 REMARK 3 BIN FREE R VALUE SET COUNT : 55 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6532 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 77 REMARK 3 SOLVENT ATOMS : 747 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.79000 REMARK 3 B22 (A**2) : 0.79000 REMARK 3 B33 (A**2) : -1.57000 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): 0.121 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.113 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.070 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.532 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6913 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 6268 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9371 ; 1.184 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14542 ; 1.324 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 822 ; 5.655 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 358 ;34.628 ;23.520 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1218 ;13.395 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 63 ;16.728 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 997 ; 0.151 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7684 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1475 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1274 ; 0.206 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 6013 ; 0.167 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3215 ; 0.172 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 3581 ; 0.080 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 434 ; 0.164 ; 0.200 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): 8 ; 0.083 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 65 ; 0.243 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 34 ; 0.114 ; 0.200 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): 5373 ; 0.692 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1646 ; 0.103 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6595 ; 0.756 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3347 ; 1.241 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2776 ; 1.779 ; 4.500 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 : 1 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 958 A 1600 REMARK 3 ORIGIN FOR THE GROUP (A): 21.3964 99.8181 2.4133 REMARK 3 T TENSOR REMARK 3 T11: -0.0279 T22: -0.0322 REMARK 3 T33: -0.0171 T12: 0.0466 REMARK 3 T13: -0.0135 T23: -0.0084 REMARK 3 L TENSOR REMARK 3 L11: 0.1260 L22: 0.1614 REMARK 3 L33: 0.3420 L12: -0.0402 REMARK 3 L13: -0.0090 L23: 0.0042 REMARK 3 S TENSOR REMARK 3 S11: -0.0128 S12: 0.0089 S13: 0.0000 REMARK 3 S21: -0.0211 S22: -0.0141 S23: 0.0055 REMARK 3 S31: -0.0107 S32: -0.0346 S33: 0.0269 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK 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 2GJ4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-APR-06. REMARK 100 THE RCSB ID CODE IS RCSB037181. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-OCT-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87 REMARK 200 MONOCHROMATOR : TRIANGULAR SINGLE CRYSTAL SI REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : RH COATED SI MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : ADSC REMARK 200 DATA SCALING SOFTWARE : MOSFLM REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 94754 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 48.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 74.5 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : 0.04500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.5 REMARK 200 DATA REDUNDANCY IN SHELL : 1.40 REMARK 200 R MERGE FOR SHELL (I) : 0.46600 REMARK 200 R SYM FOR SHELL (I) : 0.63700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: IN HOUSE MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.1MM IMP, 1.1MM SPERMINE, 0MM BES, REMARK 280 2.9MM DTT, 0.1MM EDTA, PH 6.7, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 58.17300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 64.06400 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 64.06400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 87.25950 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 64.06400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 64.06400 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.08650 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 64.06400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 64.06400 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 87.25950 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 64.06400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 64.06400 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 29.08650 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 58.17300 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 10250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 57450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -293.0 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 0.000000 -1.000000 0.000000 128.12800 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 128.12800 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 58.17300 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 A1681 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1675 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 ASP A 251 REMARK 465 PHE A 252 REMARK 465 ASN A 253 REMARK 465 LEU A 254 REMARK 465 LYS A 255 REMARK 465 ASP A 256 REMARK 465 PHE A 257 REMARK 465 ASN A 258 REMARK 465 VAL A 259 REMARK 465 GLY A 260 REMARK 465 SER A 314 REMARK 465 LYS A 315 REMARK 465 PHE A 316 REMARK 465 GLY A 317 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 THR A 324 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 GLN A 12 CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 956 O HOH A 1676 1.75 REMARK 500 O HOH A 956 O HOH A 1680 1.76 REMARK 500 O HOH A 1194 O HOH A 1693 2.03 REMARK 500 O HOH A 1185 O HOH A 1692 2.11 REMARK 500 O HOH A 1231 O HOH A 1692 2.13 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 ALA A 19 74.83 -107.53 REMARK 500 LEU A 131 38.70 -91.25 REMARK 500 TYR A 203 -135.65 63.01 REMARK 500 THR A 209 -166.97 -104.08 REMARK 500 ASP A 283 -74.92 -95.86 REMARK 500 ASN A 284 67.31 -112.18 REMARK 500 ASP A 339 -169.86 68.59 REMARK 500 THR A 466 -68.58 -129.29 REMARK 500 ARG A 489 -72.36 -72.35 REMARK 500 LEU A 492 -62.30 -145.18 REMARK 500 ASP A 514 65.17 -161.08 REMARK 500 ASN A 560 52.42 -99.56 REMARK 500 LYS A 568 165.78 170.44 REMARK 500 SER A 674 -60.48 -139.80 REMARK 500 SER A 751 63.94 -151.59 REMARK 500 ILE A 824 -53.44 -123.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ASN A 284 1.7 L L EXPECTING SP3 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1271 DISTANCE = 5.06 ANGSTROMS REMARK 525 HOH A1417 DISTANCE = 5.47 ANGSTROMS REMARK 525 HOH A1471 DISTANCE = 5.53 ANGSTROMS REMARK 525 HOH A1477 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH A1487 DISTANCE = 5.67 ANGSTROMS REMARK 525 HOH A1532 DISTANCE = 6.85 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 941 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 942 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 943 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 944 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 945 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 946 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 947 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 948 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLR A 940 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2TH A 949 DBREF 2GJ4 A 12 835 UNP P00489 PYGM_RABIT 12 835 SEQRES 1 A 824 GLN ILE SER VAL ARG GLY LEU ALA GLY VAL GLU ASN VAL SEQRES 2 A 824 THR GLU LEU LYS LYS ASN PHE ASN ARG HIS LEU HIS PHE SEQRES 3 A 824 THR LEU VAL LYS ASP ARG ASN VAL ALA THR PRO ARG ASP SEQRES 4 A 824 TYR TYR PHE ALA LEU ALA HIS THR VAL ARG ASP HIS LEU SEQRES 5 A 824 VAL GLY ARG TRP ILE ARG THR GLN GLN HIS TYR TYR GLU SEQRES 6 A 824 LYS ASP PRO LYS ARG ILE TYR TYR LEU SER LEU GLU PHE SEQRES 7 A 824 TYR MET GLY ARG THR LEU GLN ASN THR MET VAL ASN LEU SEQRES 8 A 824 ALA LEU GLU ASN ALA CYS ASP GLU ALA THR TYR GLN LEU SEQRES 9 A 824 GLY LEU ASP MET GLU GLU LEU GLU GLU ILE GLU GLU ASP SEQRES 10 A 824 ALA GLY LEU GLY ASN GLY GLY LEU GLY ARG LEU ALA ALA SEQRES 11 A 824 CYS PHE LEU ASP SER MET ALA THR LEU GLY LEU ALA ALA SEQRES 12 A 824 TYR GLY TYR GLY ILE ARG TYR GLU PHE GLY ILE PHE ASN SEQRES 13 A 824 GLN LYS ILE CYS GLY GLY TRP GLN MET GLU GLU ALA ASP SEQRES 14 A 824 ASP TRP LEU ARG TYR GLY ASN PRO TRP GLU LYS ALA ARG SEQRES 15 A 824 PRO GLU PHE THR LEU PRO VAL HIS PHE TYR GLY ARG VAL SEQRES 16 A 824 GLU HIS THR SER GLN GLY ALA LYS TRP VAL ASP THR GLN SEQRES 17 A 824 VAL VAL LEU ALA MET PRO TYR ASP THR PRO VAL PRO GLY SEQRES 18 A 824 TYR ARG ASN ASN VAL VAL ASN THR MET ARG LEU TRP SER SEQRES 19 A 824 ALA LYS ALA PRO ASN ASP PHE ASN LEU LYS ASP PHE ASN SEQRES 20 A 824 VAL GLY GLY TYR ILE GLN ALA VAL LEU ASP ARG ASN LEU SEQRES 21 A 824 ALA GLU ASN ILE SER ARG VAL LEU TYR PRO ASN ASP ASN SEQRES 22 A 824 PHE PHE GLU GLY LYS GLU LEU ARG LEU LYS GLN GLU TYR SEQRES 23 A 824 PHE VAL VAL ALA ALA THR LEU GLN ASP ILE ILE ARG ARG SEQRES 24 A 824 PHE LYS SER SER LYS PHE GLY CYS ARG ASP PRO VAL ARG SEQRES 25 A 824 THR ASN PHE ASP ALA PHE PRO ASP LYS VAL ALA ILE GLN SEQRES 26 A 824 LEU ASN ASP THR HIS PRO SER LEU ALA ILE PRO GLU LEU SEQRES 27 A 824 MET ARG VAL LEU VAL ASP LEU GLU ARG LEU ASP TRP ASP SEQRES 28 A 824 LYS ALA TRP GLU VAL THR VAL LYS THR CYS ALA TYR THR SEQRES 29 A 824 ASN HIS THR VAL LEU PRO GLU ALA LEU GLU ARG TRP PRO SEQRES 30 A 824 VAL HIS LEU LEU GLU THR LEU LEU PRO ARG HIS LEU GLN SEQRES 31 A 824 ILE ILE TYR GLU ILE ASN GLN ARG PHE LEU ASN ARG VAL SEQRES 32 A 824 ALA ALA ALA PHE PRO GLY ASP VAL ASP ARG LEU ARG ARG SEQRES 33 A 824 MET SER LEU VAL GLU GLU GLY ALA VAL LYS ARG ILE ASN SEQRES 34 A 824 MET ALA HIS LEU CYS ILE ALA GLY SER HIS ALA VAL ASN SEQRES 35 A 824 GLY VAL ALA ARG ILE HIS SER GLU ILE LEU LYS LYS THR SEQRES 36 A 824 ILE PHE LYS ASP PHE TYR GLU LEU GLU PRO HIS LYS PHE SEQRES 37 A 824 GLN ASN LYS THR ASN GLY ILE THR PRO ARG ARG TRP LEU SEQRES 38 A 824 VAL LEU CYS ASN PRO GLY LEU ALA GLU ILE ILE ALA GLU SEQRES 39 A 824 ARG ILE GLY GLU GLU TYR ILE SER ASP LEU ASP GLN LEU SEQRES 40 A 824 ARG LYS LEU LEU SER TYR VAL ASP ASP GLU ALA PHE ILE SEQRES 41 A 824 ARG ASP VAL ALA LYS VAL LYS GLN GLU ASN LYS LEU LYS SEQRES 42 A 824 PHE ALA ALA TYR LEU GLU ARG GLU TYR LYS VAL HIS ILE SEQRES 43 A 824 ASN PRO ASN SER LEU PHE ASP VAL GLN VAL LYS ARG ILE SEQRES 44 A 824 HIS GLU TYR LYS ARG GLN LEU LEU ASN CYS LEU HIS VAL SEQRES 45 A 824 ILE THR LEU TYR ASN ARG ILE LYS LYS GLU PRO ASN LYS SEQRES 46 A 824 PHE VAL VAL PRO ARG THR VAL MET ILE GLY GLY LYS ALA SEQRES 47 A 824 ALA PRO GLY TYR HIS MET ALA LYS MET ILE ILE LYS LEU SEQRES 48 A 824 ILE THR ALA ILE GLY ASP VAL VAL ASN HIS ASP PRO VAL SEQRES 49 A 824 VAL GLY ASP ARG LEU ARG VAL ILE PHE LEU GLU ASN TYR SEQRES 50 A 824 ARG VAL SER LEU ALA GLU LYS VAL ILE PRO ALA ALA ASP SEQRES 51 A 824 LEU SER GLU GLN ILE SER THR ALA GLY THR GLU ALA SER SEQRES 52 A 824 GLY THR GLY ASN MET LYS PHE MET LEU ASN GLY ALA LEU SEQRES 53 A 824 THR ILE GLY THR MET ASP GLY ALA ASN VAL GLU MET ALA SEQRES 54 A 824 GLU GLU ALA GLY GLU GLU ASN PHE PHE ILE PHE GLY MET SEQRES 55 A 824 ARG VAL GLU ASP VAL ASP ARG LEU ASP GLN ARG GLY TYR SEQRES 56 A 824 ASN ALA GLN GLU TYR TYR ASP ARG ILE PRO GLU LEU ARG SEQRES 57 A 824 GLN ILE ILE GLU GLN LEU SER SER GLY PHE PHE SER PRO SEQRES 58 A 824 LYS GLN PRO ASP LEU PHE LYS ASP ILE VAL ASN MET LEU SEQRES 59 A 824 MET HIS HIS ASP ARG PHE LYS VAL PHE ALA ASP TYR GLU SEQRES 60 A 824 GLU TYR VAL LYS CYS GLN GLU ARG VAL SER ALA LEU TYR SEQRES 61 A 824 LYS ASN PRO ARG GLU TRP THR ARG MET VAL ILE ARG ASN SEQRES 62 A 824 ILE ALA THR SER GLY LYS PHE SER SER ASP ARG THR ILE SEQRES 63 A 824 ALA GLN TYR ALA ARG GLU ILE TRP GLY VAL GLU PRO SER SEQRES 64 A 824 ARG GLN ARG LEU PRO HET SO4 A 941 5 HET SO4 A 942 5 HET SO4 A 943 5 HET SO4 A 944 5 HET SO4 A 945 5 HET SO4 A 946 5 HET SO4 A 947 5 HET SO4 A 948 5 HET PLR A 940 15 HET 2TH A 949 22 HETNAM SO4 SULFATE ION HETNAM PLR (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN HETNAM 2 PLR PHOSPHATE HETNAM 2TH 2-CHLORO-N-[(1R,2R)-1-HYDROXY-2,3-DIHYDRO-1H-INDEN-2- HETNAM 2 2TH YL]-6H-THIENO[2,3-B]PYRROLE-5-CARBOXAMIDE HETSYN PLR 4'-DEOXYPYRIDOXINE PHOSPHATE FORMUL 2 SO4 8(O4 S 2-) FORMUL 10 PLR C8 H12 N O5 P FORMUL 11 2TH C16 H13 CL N2 O2 S FORMUL 12 HOH *747(H2 O) HELIX 1 1 ILE A 13 GLY A 17 5 5 HELIX 2 2 GLY A 20 THR A 38 1 19 HELIX 3 3 THR A 47 HIS A 62 1 16 HELIX 4 4 LEU A 63 ASP A 78 1 16 HELIX 5 5 THR A 94 LEU A 102 1 9 HELIX 6 6 LEU A 104 LEU A 115 1 12 HELIX 7 7 ASP A 118 GLU A 124 1 7 HELIX 8 8 GLY A 134 LEU A 150 1 17 HELIX 9 9 PRO A 194 THR A 197 5 4 HELIX 10 10 GLY A 261 ASP A 268 1 8 HELIX 11 11 ASP A 268 ASN A 274 1 7 HELIX 12 12 ILE A 275 ARG A 277 5 3 HELIX 13 13 LYS A 289 SER A 313 1 25 HELIX 14 14 ASN A 325 ASP A 327 5 3 HELIX 15 15 ALA A 328 LYS A 332 1 5 HELIX 16 16 LEU A 344 LEU A 356 1 13 HELIX 17 17 ASP A 360 THR A 371 1 12 HELIX 18 18 LEU A 380 LEU A 384 5 5 HELIX 19 19 VAL A 389 LEU A 396 1 8 HELIX 20 20 LEU A 396 PHE A 418 1 23 HELIX 21 21 ASP A 421 SER A 429 1 9 HELIX 22 22 MET A 441 GLY A 448 1 8 HELIX 23 23 ALA A 456 THR A 466 1 11 HELIX 24 24 PHE A 468 GLU A 475 1 8 HELIX 25 25 ASN A 496 GLY A 508 1 13 HELIX 26 26 GLU A 509 VAL A 525 5 17 HELIX 27 27 ASP A 527 LYS A 554 1 28 HELIX 28 28 ARG A 575 GLU A 593 1 19 HELIX 29 29 TYR A 613 ASN A 631 1 19 HELIX 30 30 VAL A 636 ASP A 638 5 3 HELIX 31 31 ARG A 649 ILE A 657 1 9 HELIX 32 32 PRO A 658 ALA A 660 5 3 HELIX 33 33 THR A 676 ASN A 684 1 9 HELIX 34 34 ALA A 695 GLY A 704 1 10 HELIX 35 35 GLU A 705 PHE A 708 5 4 HELIX 36 36 ARG A 714 GLY A 725 1 12 HELIX 37 37 ASN A 727 ILE A 735 1 9 HELIX 38 38 ILE A 735 GLY A 748 1 14 HELIX 39 39 PHE A 758 HIS A 768 1 11 HELIX 40 40 VAL A 773 ALA A 775 5 3 HELIX 41 41 ASP A 776 LYS A 792 1 17 HELIX 42 42 ASN A 793 ALA A 806 1 14 HELIX 43 43 THR A 807 PHE A 811 5 5 HELIX 44 44 SER A 812 ILE A 824 1 13 SHEET 1 A 3 LYS A 191 ALA A 192 0 SHEET 2 A 3 GLN A 219 PRO A 231 -1 O ASP A 227 N LYS A 191 SHEET 3 A 3 LEU A 198 PHE A 202 -1 N LEU A 198 O ALA A 223 SHEET 1 B 9 LYS A 191 ALA A 192 0 SHEET 2 B 9 GLN A 219 PRO A 231 -1 O ASP A 227 N LYS A 191 SHEET 3 B 9 VAL A 238 LYS A 247 -1 O SER A 245 N MET A 224 SHEET 4 B 9 ALA A 154 ILE A 159 1 N GLY A 156 O ARG A 242 SHEET 5 B 9 ARG A 81 LEU A 85 1 N ILE A 82 O TYR A 155 SHEET 6 B 9 VAL A 333 ASN A 338 1 O GLN A 336 N TYR A 83 SHEET 7 B 9 CYS A 372 THR A 375 1 O ALA A 373 N LEU A 337 SHEET 8 B 9 VAL A 452 GLY A 454 1 O ASN A 453 N TYR A 374 SHEET 9 B 9 PHE A 479 ASN A 481 1 O GLN A 480 N VAL A 452 SHEET 1 C 2 PHE A 89 GLY A 92 0 SHEET 2 C 2 ALA A 129 LEU A 131 -1 O LEU A 131 N PHE A 89 SHEET 1 D 2 ASN A 167 CYS A 171 0 SHEET 2 D 2 TRP A 174 GLU A 178 -1 O MET A 176 N LYS A 169 SHEET 1 E 2 ARG A 205 HIS A 208 0 SHEET 2 E 2 ALA A 213 VAL A 216 -1 O VAL A 216 N ARG A 205 SHEET 1 F 3 ARG A 386 PRO A 388 0 SHEET 2 F 3 ARG A 438 ASN A 440 -1 O ILE A 439 N TRP A 387 SHEET 3 F 3 VAL A 431 GLU A 432 -1 N GLU A 432 O ARG A 438 SHEET 1 G 6 LEU A 640 LEU A 645 0 SHEET 2 G 6 ARG A 601 GLY A 606 1 N VAL A 603 O ARG A 641 SHEET 3 G 6 LEU A 562 VAL A 567 1 N ASP A 564 O MET A 604 SHEET 4 G 6 LEU A 662 GLN A 665 1 O LEU A 662 N VAL A 565 SHEET 5 G 6 LEU A 687 GLY A 690 1 O LEU A 687 N SER A 663 SHEET 6 G 6 PHE A 709 ILE A 710 1 O PHE A 709 N THR A 688 LINK NZ LYS A 680 C4A PLR A 940 1555 1555 1.71 SITE 1 AC1 5 TRP A 67 GLN A 71 ARG A 193 HOH A1290 SITE 2 AC1 5 HOH A1331 SITE 1 AC2 4 TRP A 215 ARG A 351 HOH A1029 HOH A1447 SITE 1 AC3 5 GLN A 219 VAL A 221 ALA A 272 ILE A 275 SITE 2 AC3 5 LYS A 294 SITE 1 AC4 2 PHE A 37 HIS A 62 SITE 1 AC5 8 LEU A 549 TYR A 553 ILE A 643 PHE A 644 SITE 2 AC5 8 LEU A 645 GLU A 646 HOH A1091 HOH A1437 SITE 1 AC6 6 GLU A 706 PHE A 708 PHE A 709 ARG A 786 SITE 2 AC6 6 HOH A1216 HOH A1595 SITE 1 AC7 5 ARG A 519 GLU A 702 ALA A 703 THR A 807 SITE 2 AC7 5 HOH A1080 SITE 1 AC8 4 GLN A 408 LEU A 411 ASN A 412 ALA A 415 SITE 1 AC9 17 TYR A 90 GLY A 134 LYS A 568 LYS A 574 SITE 2 AC9 17 TYR A 648 ARG A 649 VAL A 650 GLY A 675 SITE 3 AC9 17 THR A 676 GLY A 677 LYS A 680 HOH A 958 SITE 4 AC9 17 HOH A 974 HOH A 979 HOH A1001 HOH A1020 SITE 5 AC9 17 HOH A1321 SITE 1 BC1 11 THR A 38 VAL A 40 HIS A 57 ARG A 60 SITE 2 BC1 11 TRP A 67 GLU A 190 LYS A 191 HOH A 975 SITE 3 BC1 11 HOH A1065 HOH A1102 HOH A1674 CRYST1 128.128 128.128 116.346 90.00 90.00 90.00 P 43 21 2 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 0.007805 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007805 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008595 0.00000