HEADER LYASE 17-OCT-08 3EXS TITLE CRYSTAL STRUCTURE OF KGPDC FROM STREPTOCOCCUS MUTANS IN COMPLEX WITH TITLE 2 D-R5P COMPND MOL_ID: 1; COMPND 2 MOLECULE: RMPD (HEXULOSE-6-PHOSPHATE SYNTHASE); COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: 3-KETO-L-GULONATE 6-PHOSPHATE DECARBOXYLASE; COMPND 5 EC: 4.1.1.85; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS MUTANS; SOURCE 3 ORGANISM_TAXID: 1309; SOURCE 4 GENE: ULAD; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS BETA BARREL, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR G.L.LI,X.LIU,K.T.WANG,L.F.LI,X.D.SU REVDAT 2 01-NOV-23 3EXS 1 REMARK REVDAT 1 25-AUG-09 3EXS 0 JRNL AUTH G.L.LI,X.LIU,J.NAN,E.BROSTROMER,L.F.LI,X.D.SU JRNL TITL OPEN-CLOSED CONFORMATIONAL CHANGE REVEALED BY THE CRYSTAL JRNL TITL 2 STRUCTURES OF 3-KETO-L-GULONATE 6-PHOSPHATE DECARBOXYLASE JRNL TITL 3 FROM STREPTOCOCCUS MUTANS JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 381 429 2009 JRNL REFN ISSN 0006-291X JRNL PMID 19222992 JRNL DOI 10.1016/J.BBRC.2009.02.049 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.9 REMARK 3 NUMBER OF REFLECTIONS : 29234 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1548 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) : 1289 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 55.43 REMARK 3 BIN R VALUE (WORKING SET) : 0.2610 REMARK 3 BIN FREE R VALUE SET COUNT : 58 REMARK 3 BIN FREE R VALUE : 0.3490 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6335 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 298 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.28000 REMARK 3 B22 (A**2) : -0.34000 REMARK 3 B33 (A**2) : 0.62000 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): 0.775 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.306 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.202 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.172 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.934 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.878 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6459 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8761 ; 1.367 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 840 ; 6.789 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 264 ;36.350 ;25.379 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1091 ;17.396 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;24.645 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1029 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4778 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3122 ; 0.221 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4483 ; 0.308 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 394 ; 0.178 ; 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): 21 ; 0.123 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.140 ; 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): 4249 ; 0.813 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6658 ; 1.240 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2492 ; 1.901 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2103 ; 3.014 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 3EXS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-OCT-08. REMARK 100 THE DEPOSITION ID IS D_1000049900. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAY-08 REMARK 200 TEMPERATURE (KELVIN) : 100 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 : OTHER REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER SMART 6000 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SAINT REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31798 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 19.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07700 REMARK 200 FOR THE DATA SET : NULL 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 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: NULL REMARK 200 STARTING MODEL: PDB ENTRY 3EXT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M KCL, 0.05M HEPES, PH7.5, 35%(V/V) REMARK 280 PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH), VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 29.57600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 65.03300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 62.12450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 65.03300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.57600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 62.12450 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 2740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.3 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 REMARK 350 BIOMOLECULE: 2 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: 2970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 LYS A 3 REMARK 465 GLN A 4 REMARK 465 ASP A 145 REMARK 465 ALA A 146 REMARK 465 LEU A 147 REMARK 465 LEU A 148 REMARK 465 ALA A 149 REMARK 465 GLY A 150 REMARK 465 GLU A 151 REMARK 465 THR A 152 REMARK 465 TRP A 153 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 LYS B 3 REMARK 465 ASP B 145 REMARK 465 ALA B 146 REMARK 465 LEU B 147 REMARK 465 LEU B 148 REMARK 465 ALA B 149 REMARK 465 GLY B 150 REMARK 465 GLU B 151 REMARK 465 MET C 1 REMARK 465 THR C 2 REMARK 465 LYS C 3 REMARK 465 GLN C 4 REMARK 465 ASP C 145 REMARK 465 ALA C 146 REMARK 465 LEU C 147 REMARK 465 LEU C 148 REMARK 465 ALA C 149 REMARK 465 GLY C 150 REMARK 465 GLU C 151 REMARK 465 THR C 152 REMARK 465 TRP C 153 REMARK 465 MET D 1 REMARK 465 THR D 2 REMARK 465 LYS D 3 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 LYS A 156 CG CD CE NZ REMARK 470 LYS A 183 CG CD CE NZ REMARK 470 GLN B 4 CG CD OE1 NE2 REMARK 470 ASP B 106 CG OD1 OD2 REMARK 470 ARG B 144 CZ NH1 NH2 REMARK 470 LYS B 156 CG CD CE NZ REMARK 470 ARG B 197 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 203 CG CD CE NZ REMARK 470 GLU B 215 CG CD OE1 OE2 REMARK 470 LYS C 156 CG CD CE NZ REMARK 470 LYS C 203 CG CD CE NZ REMARK 470 GLN D 4 CG CD OE1 NE2 REMARK 470 LYS D 156 CG CD CE NZ REMARK 470 LYS D 203 CG CD CE NZ 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 CG2 THR B 152 O HOH B 256 1.96 REMARK 500 O LYS B 203 O HOH B 244 1.98 REMARK 500 OD2 ASP A 58 O HOH A 258 2.14 REMARK 500 O ARG C 144 O HOH C 282 2.15 REMARK 500 N THR B 152 O HOH B 284 2.19 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 ARG D 144 CA - CB - CG ANGL. DEV. = 14.8 DEGREES REMARK 500 ARG D 144 CA - CB - CG ANGL. DEV. = 14.4 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 LEU A 184 2.82 -69.78 REMARK 500 ASN A 204 78.86 -119.34 REMARK 500 TRP B 153 94.55 -50.03 REMARK 500 ALA B 202 156.12 -46.84 REMARK 500 LYS C 111 -7.33 -143.76 REMARK 500 ALA C 202 -136.95 -142.26 REMARK 500 ASN C 204 51.19 37.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 THR C 200 GLU C 201 146.62 REMARK 500 ALA C 202 LYS C 203 60.12 REMARK 500 LYS C 203 ASN C 204 -133.85 REMARK 500 HIS D 141 GLN D 142 142.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 5RP D 502 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 5RP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 5RP D 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3EXR RELATED DB: PDB REMARK 900 RELATED ID: 3EXT RELATED DB: PDB DBREF 3EXS A 1 221 UNP Q93DA8 Q93DA8_STRMU 1 221 DBREF 3EXS B 1 221 UNP Q93DA8 Q93DA8_STRMU 1 221 DBREF 3EXS C 1 221 UNP Q93DA8 Q93DA8_STRMU 1 221 DBREF 3EXS D 1 221 UNP Q93DA8 Q93DA8_STRMU 1 221 SEQRES 1 A 221 MET THR LYS GLN LEU PRO ASN LEU GLN VAL ALA LEU ASP SEQRES 2 A 221 HIS SER ASN LEU LYS GLY ALA ILE THR ALA ALA VAL SER SEQRES 3 A 221 VAL GLY ASN GLU VAL ASP VAL ILE GLU ALA GLY THR VAL SEQRES 4 A 221 CYS LEU LEU GLN VAL GLY SER GLU LEU VAL GLU VAL LEU SEQRES 5 A 221 ARG SER LEU PHE PRO ASP LYS ILE ILE VAL ALA ASP THR SEQRES 6 A 221 LYS CYS ALA ASP ALA GLY GLY THR VAL ALA LYS ASN ASN SEQRES 7 A 221 ALA VAL ARG GLY ALA ASP TRP MET THR CYS ILE CYS SER SEQRES 8 A 221 ALA THR ILE PRO THR MET LYS ALA ALA ARG LYS ALA ILE SEQRES 9 A 221 GLU ASP ILE ASN PRO ASP LYS GLY GLU ILE GLN VAL GLU SEQRES 10 A 221 LEU TYR GLY ASP TRP THR TYR ASP GLN ALA GLN GLN TRP SEQRES 11 A 221 LEU ASP ALA GLY ILE SER GLN ALA ILE TYR HIS GLN SER SEQRES 12 A 221 ARG ASP ALA LEU LEU ALA GLY GLU THR TRP GLY GLU LYS SEQRES 13 A 221 ASP LEU ASN LYS VAL LYS LYS LEU ILE GLU MET GLY PHE SEQRES 14 A 221 ARG VAL SER VAL THR GLY GLY LEU SER VAL ASP THR LEU SEQRES 15 A 221 LYS LEU PHE GLU GLY VAL ASP VAL PHE THR PHE ILE ALA SEQRES 16 A 221 GLY ARG GLY ILE THR GLU ALA LYS ASN PRO ALA GLY ALA SEQRES 17 A 221 ALA ARG ALA PHE LYS ASP GLU ILE LYS ARG ILE TRP GLY SEQRES 1 B 221 MET THR LYS GLN LEU PRO ASN LEU GLN VAL ALA LEU ASP SEQRES 2 B 221 HIS SER ASN LEU LYS GLY ALA ILE THR ALA ALA VAL SER SEQRES 3 B 221 VAL GLY ASN GLU VAL ASP VAL ILE GLU ALA GLY THR VAL SEQRES 4 B 221 CYS LEU LEU GLN VAL GLY SER GLU LEU VAL GLU VAL LEU SEQRES 5 B 221 ARG SER LEU PHE PRO ASP LYS ILE ILE VAL ALA ASP THR SEQRES 6 B 221 LYS CYS ALA ASP ALA GLY GLY THR VAL ALA LYS ASN ASN SEQRES 7 B 221 ALA VAL ARG GLY ALA ASP TRP MET THR CYS ILE CYS SER SEQRES 8 B 221 ALA THR ILE PRO THR MET LYS ALA ALA ARG LYS ALA ILE SEQRES 9 B 221 GLU ASP ILE ASN PRO ASP LYS GLY GLU ILE GLN VAL GLU SEQRES 10 B 221 LEU TYR GLY ASP TRP THR TYR ASP GLN ALA GLN GLN TRP SEQRES 11 B 221 LEU ASP ALA GLY ILE SER GLN ALA ILE TYR HIS GLN SER SEQRES 12 B 221 ARG ASP ALA LEU LEU ALA GLY GLU THR TRP GLY GLU LYS SEQRES 13 B 221 ASP LEU ASN LYS VAL LYS LYS LEU ILE GLU MET GLY PHE SEQRES 14 B 221 ARG VAL SER VAL THR GLY GLY LEU SER VAL ASP THR LEU SEQRES 15 B 221 LYS LEU PHE GLU GLY VAL ASP VAL PHE THR PHE ILE ALA SEQRES 16 B 221 GLY ARG GLY ILE THR GLU ALA LYS ASN PRO ALA GLY ALA SEQRES 17 B 221 ALA ARG ALA PHE LYS ASP GLU ILE LYS ARG ILE TRP GLY SEQRES 1 C 221 MET THR LYS GLN LEU PRO ASN LEU GLN VAL ALA LEU ASP SEQRES 2 C 221 HIS SER ASN LEU LYS GLY ALA ILE THR ALA ALA VAL SER SEQRES 3 C 221 VAL GLY ASN GLU VAL ASP VAL ILE GLU ALA GLY THR VAL SEQRES 4 C 221 CYS LEU LEU GLN VAL GLY SER GLU LEU VAL GLU VAL LEU SEQRES 5 C 221 ARG SER LEU PHE PRO ASP LYS ILE ILE VAL ALA ASP THR SEQRES 6 C 221 LYS CYS ALA ASP ALA GLY GLY THR VAL ALA LYS ASN ASN SEQRES 7 C 221 ALA VAL ARG GLY ALA ASP TRP MET THR CYS ILE CYS SER SEQRES 8 C 221 ALA THR ILE PRO THR MET LYS ALA ALA ARG LYS ALA ILE SEQRES 9 C 221 GLU ASP ILE ASN PRO ASP LYS GLY GLU ILE GLN VAL GLU SEQRES 10 C 221 LEU TYR GLY ASP TRP THR TYR ASP GLN ALA GLN GLN TRP SEQRES 11 C 221 LEU ASP ALA GLY ILE SER GLN ALA ILE TYR HIS GLN SER SEQRES 12 C 221 ARG ASP ALA LEU LEU ALA GLY GLU THR TRP GLY GLU LYS SEQRES 13 C 221 ASP LEU ASN LYS VAL LYS LYS LEU ILE GLU MET GLY PHE SEQRES 14 C 221 ARG VAL SER VAL THR GLY GLY LEU SER VAL ASP THR LEU SEQRES 15 C 221 LYS LEU PHE GLU GLY VAL ASP VAL PHE THR PHE ILE ALA SEQRES 16 C 221 GLY ARG GLY ILE THR GLU ALA LYS ASN PRO ALA GLY ALA SEQRES 17 C 221 ALA ARG ALA PHE LYS ASP GLU ILE LYS ARG ILE TRP GLY SEQRES 1 D 221 MET THR LYS GLN LEU PRO ASN LEU GLN VAL ALA LEU ASP SEQRES 2 D 221 HIS SER ASN LEU LYS GLY ALA ILE THR ALA ALA VAL SER SEQRES 3 D 221 VAL GLY ASN GLU VAL ASP VAL ILE GLU ALA GLY THR VAL SEQRES 4 D 221 CYS LEU LEU GLN VAL GLY SER GLU LEU VAL GLU VAL LEU SEQRES 5 D 221 ARG SER LEU PHE PRO ASP LYS ILE ILE VAL ALA ASP THR SEQRES 6 D 221 LYS CYS ALA ASP ALA GLY GLY THR VAL ALA LYS ASN ASN SEQRES 7 D 221 ALA VAL ARG GLY ALA ASP TRP MET THR CYS ILE CYS SER SEQRES 8 D 221 ALA THR ILE PRO THR MET LYS ALA ALA ARG LYS ALA ILE SEQRES 9 D 221 GLU ASP ILE ASN PRO ASP LYS GLY GLU ILE GLN VAL GLU SEQRES 10 D 221 LEU TYR GLY ASP TRP THR TYR ASP GLN ALA GLN GLN TRP SEQRES 11 D 221 LEU ASP ALA GLY ILE SER GLN ALA ILE TYR HIS GLN SER SEQRES 12 D 221 ARG ASP ALA LEU LEU ALA GLY GLU THR TRP GLY GLU LYS SEQRES 13 D 221 ASP LEU ASN LYS VAL LYS LYS LEU ILE GLU MET GLY PHE SEQRES 14 D 221 ARG VAL SER VAL THR GLY GLY LEU SER VAL ASP THR LEU SEQRES 15 D 221 LYS LEU PHE GLU GLY VAL ASP VAL PHE THR PHE ILE ALA SEQRES 16 D 221 GLY ARG GLY ILE THR GLU ALA LYS ASN PRO ALA GLY ALA SEQRES 17 D 221 ALA ARG ALA PHE LYS ASP GLU ILE LYS ARG ILE TRP GLY HET 5RP A 501 14 HET 5RP D 502 13 HETNAM 5RP RIBULOSE-5-PHOSPHATE FORMUL 5 5RP 2(C5 H11 O8 P) FORMUL 7 HOH *298(H2 O) HELIX 1 1 ASN A 16 GLY A 28 1 13 HELIX 2 2 ASN A 29 VAL A 31 5 3 HELIX 3 3 GLY A 37 GLY A 45 1 9 HELIX 4 4 SER A 46 PHE A 56 1 11 HELIX 5 5 ALA A 70 VAL A 80 1 11 HELIX 6 6 THR A 93 ASN A 108 1 16 HELIX 7 7 THR A 123 ALA A 133 1 11 HELIX 8 8 GLY A 154 GLY A 168 1 15 HELIX 9 9 SER A 178 GLU A 186 5 9 HELIX 10 10 GLY A 196 GLU A 201 1 6 HELIX 11 11 ASN A 204 TRP A 220 1 17 HELIX 12 12 ASN B 16 GLY B 28 1 13 HELIX 13 13 ASN B 29 VAL B 31 5 3 HELIX 14 14 GLY B 37 GLY B 45 1 9 HELIX 15 15 SER B 46 PHE B 56 1 11 HELIX 16 16 ALA B 70 VAL B 80 1 11 HELIX 17 17 THR B 93 ASN B 108 1 16 HELIX 18 18 THR B 123 ALA B 133 1 11 HELIX 19 19 GLY B 154 GLY B 168 1 15 HELIX 20 20 THR B 181 GLU B 186 5 6 HELIX 21 21 GLY B 196 GLU B 201 1 6 HELIX 22 22 ASN B 204 GLY B 221 1 18 HELIX 23 23 ASN C 16 GLY C 28 1 13 HELIX 24 24 ASN C 29 VAL C 31 5 3 HELIX 25 25 GLY C 37 GLY C 45 1 9 HELIX 26 26 SER C 46 PHE C 56 1 11 HELIX 27 27 ALA C 70 VAL C 80 1 11 HELIX 28 28 THR C 93 ASN C 108 1 16 HELIX 29 29 THR C 123 ALA C 133 1 11 HELIX 30 30 GLY C 154 MET C 167 1 14 HELIX 31 31 LEU C 182 GLU C 186 5 5 HELIX 32 32 GLY C 196 GLU C 201 1 6 HELIX 33 33 ASN C 204 GLY C 221 1 18 HELIX 34 34 ASN D 16 GLY D 28 1 13 HELIX 35 35 ASN D 29 VAL D 31 5 3 HELIX 36 36 GLY D 37 GLY D 45 1 9 HELIX 37 37 SER D 46 PHE D 56 1 11 HELIX 38 38 ALA D 70 VAL D 80 1 11 HELIX 39 39 THR D 93 ASN D 108 1 16 HELIX 40 40 THR D 123 ALA D 133 1 11 HELIX 41 41 SER D 143 ALA D 149 1 7 HELIX 42 42 GLY D 154 GLY D 168 1 15 HELIX 43 43 SER D 178 GLU D 186 5 9 HELIX 44 44 GLY D 196 GLU D 201 1 6 HELIX 45 45 ASN D 204 GLY D 221 1 18 SHEET 1 A 9 ASN A 7 LEU A 12 0 SHEET 2 A 9 VAL A 33 ALA A 36 1 O GLU A 35 N LEU A 12 SHEET 3 A 9 ILE A 60 CYS A 67 1 O VAL A 62 N ALA A 36 SHEET 4 A 9 TRP A 85 ILE A 89 1 O TRP A 85 N ALA A 63 SHEET 5 A 9 GLU A 113 GLU A 117 1 O GLN A 115 N CYS A 88 SHEET 6 A 9 GLN A 137 HIS A 141 1 O GLN A 137 N VAL A 116 SHEET 7 A 9 ARG A 170 THR A 174 1 O SER A 172 N TYR A 140 SHEET 8 A 9 THR A 192 ALA A 195 1 O ILE A 194 N VAL A 173 SHEET 9 A 9 ASN A 7 LEU A 12 1 N GLN A 9 O ALA A 195 SHEET 1 B 9 ASN B 7 LEU B 12 0 SHEET 2 B 9 VAL B 33 ALA B 36 1 O GLU B 35 N LEU B 12 SHEET 3 B 9 ILE B 60 CYS B 67 1 O VAL B 62 N ILE B 34 SHEET 4 B 9 TRP B 85 ILE B 89 1 O TRP B 85 N ALA B 63 SHEET 5 B 9 GLU B 113 GLU B 117 1 O GLU B 117 N CYS B 88 SHEET 6 B 9 GLN B 137 HIS B 141 1 O GLN B 137 N VAL B 116 SHEET 7 B 9 ARG B 170 THR B 174 1 O SER B 172 N TYR B 140 SHEET 8 B 9 THR B 192 ALA B 195 1 O ILE B 194 N VAL B 173 SHEET 9 B 9 ASN B 7 LEU B 12 1 N GLN B 9 O PHE B 193 SHEET 1 C 9 ASN C 7 LEU C 12 0 SHEET 2 C 9 VAL C 33 ALA C 36 1 O GLU C 35 N LEU C 12 SHEET 3 C 9 ILE C 60 CYS C 67 1 O VAL C 62 N ILE C 34 SHEET 4 C 9 TRP C 85 ILE C 89 1 O TRP C 85 N ALA C 63 SHEET 5 C 9 GLU C 113 LEU C 118 1 O GLU C 117 N CYS C 88 SHEET 6 C 9 GLN C 137 HIS C 141 1 O ILE C 139 N VAL C 116 SHEET 7 C 9 ARG C 170 THR C 174 1 O SER C 172 N TYR C 140 SHEET 8 C 9 THR C 192 ALA C 195 1 O ILE C 194 N VAL C 173 SHEET 9 C 9 ASN C 7 LEU C 12 1 N GLN C 9 O ALA C 195 SHEET 1 D 9 ASN D 7 LEU D 12 0 SHEET 2 D 9 VAL D 33 ALA D 36 1 O GLU D 35 N LEU D 12 SHEET 3 D 9 ILE D 60 CYS D 67 1 O VAL D 62 N ALA D 36 SHEET 4 D 9 TRP D 85 ILE D 89 1 O TRP D 85 N ALA D 63 SHEET 5 D 9 GLU D 113 LEU D 118 1 O GLU D 117 N CYS D 88 SHEET 6 D 9 GLN D 137 HIS D 141 1 O ILE D 139 N VAL D 116 SHEET 7 D 9 ARG D 170 THR D 174 1 O SER D 172 N TYR D 140 SHEET 8 D 9 THR D 192 ALA D 195 1 O ILE D 194 N VAL D 173 SHEET 9 D 9 ASN D 7 LEU D 12 1 N GLN D 9 O ALA D 195 CISPEP 1 GLN D 4 LEU D 5 0 -12.50 SITE 1 AC1 12 ALA A 11 ASP A 13 LYS A 66 TYR A 119 SITE 2 AC1 12 THR A 174 GLY A 176 GLY A 196 ARG A 197 SITE 3 AC1 12 HOH A 225 HOH A 228 HOH A 262 ASP C 69 SITE 1 AC2 15 ASP B 69 ALA D 11 ASP D 13 LYS D 66 SITE 2 AC2 15 TYR D 119 HIS D 141 THR D 174 GLY D 176 SITE 3 AC2 15 GLY D 196 ARG D 197 HOH D 222 HOH D 224 SITE 4 AC2 15 HOH D 226 HOH D 262 HOH D 289 CRYST1 59.152 124.249 130.066 90.00 90.00 90.00 P 21 21 21 16 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 0.016906 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008048 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007688 0.00000