HEADER LYASE 06-JAN-03 1OAB TITLE CRYSTAL STRUCTURE OF THE TYROSINE REGULATED 3-DEOXY-D-ARABINO- TITLE 2 HEPTULOSONATE-7-PHOSPHATE SYNTHASE FROM SACCHAROMYCES CEREVISIAE IN TITLE 3 COMPLEX WITH PHOSPHOENOLPYRUVATE AND MANGANESE(II) COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7- COMPND 3 PHOSPHATE SYNTHASE; COMPND 4 CHAIN: A, B; COMPND 5 SYNONYM: PHOSPHO-2-KETO-3-DEOXYHEPTONATE ALDOLASE, DAHP SYNTHETASE, COMPND 6 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE, PHOSPHO-2- COMPND 7 DEHYDRO-3-DEOXYHEPTONATE ALDOLASE TYROSINE-INHIBITED, PHOSPHO-2- COMPND 8 DEHYDRO-3-DEOXYHEPTONATE ALDOLASE; COMPND 9 EC: 4.1.2.15; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 STRAIN: RH1326; SOURCE 6 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4932 KEYWDS BETA-ALPHA-BARREL, LYASE, SYNTHASE EXPDTA X-RAY DIFFRACTION AUTHOR V.KOENIG,A.PFEIL,G.HEINRICH,G.H.BRAUS,T.R.SCHNEIDER REVDAT 4 13-DEC-23 1OAB 1 REMARK LINK REVDAT 3 24-FEB-09 1OAB 1 VERSN REVDAT 2 26-MAY-05 1OAB 1 AUTHOR JRNL REVDAT 1 23-JAN-04 1OAB 0 JRNL AUTH V.KOENIG,A.PFEIL,G.H.BRAUS,T.R.SCHNEIDER JRNL TITL SUBSTRATE AND METAL COMPLEXES OF JRNL TITL 2 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE FROM JRNL TITL 3 SACCHAROMYCES CEREVISIAE PROVIDE NEW INSIGHTS INTO THE JRNL TITL 4 CATALYTIC MECHANISM JRNL REF J.MOL.BIOL. V. 337 675 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15019786 JRNL DOI 10.1016/J.JMB.2004.01.055 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.08 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 45985 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) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2424 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3363 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2660 REMARK 3 BIN FREE R VALUE SET COUNT : 172 REMARK 3 BIN FREE R VALUE : 0.3810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5160 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 417 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.13000 REMARK 3 B22 (A**2) : 0.07000 REMARK 3 B33 (A**2) : -0.08000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.22000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.150 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.136 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.087 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.969 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5253 ; 0.025 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7111 ; 2.032 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 678 ; 5.868 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 228 ;37.035 ;24.825 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 910 ;14.620 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;18.204 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 824 ; 0.245 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3930 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2756 ; 0.215 ; 0.200 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): 500 ; 0.140 ; 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): 49 ; 0.205 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 12 ; 0.319 ; 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): 3368 ; 1.114 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5407 ; 1.878 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1885 ; 3.320 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1704 ; 5.207 ; 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 : BABINET MODEL WITH 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: NULL REMARK 4 REMARK 4 1OAB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-JAN-03. REMARK 100 THE DEPOSITION ID IS D_1290011829. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-00 REMARK 200 TEMPERATURE (KELVIN) : 105.0 REMARK 200 PH : 8.00 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 : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 178093 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.630 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.3400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.38000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: PDB ENTRY 1HFB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS PH 7.5-9.0 10 MM, 20% PEG3400, 5% REMARK 280 GLYCEROL, 4 EQUIV. PEP, 13-17MG/ML DAHPS, PH 8.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 98.31800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.25100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 98.31800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.25100 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: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 SER A 2 REMARK 465 GLU A 3 REMARK 465 SER A 4 REMARK 465 PRO A 5 REMARK 465 MET A 6 REMARK 465 PHE A 7 REMARK 465 ALA A 8 REMARK 465 ALA A 9 REMARK 465 ASN A 10 REMARK 465 GLY A 11 REMARK 465 MET A 12 REMARK 465 PRO A 13 REMARK 465 LYS A 14 REMARK 465 VAL A 15 REMARK 465 ASN A 16 REMARK 465 GLN A 17 REMARK 465 GLY A 18 REMARK 465 ALA A 19 REMARK 465 GLU A 20 REMARK 465 GLU A 21 REMARK 465 ASP A 22 REMARK 465 ALA A 328 REMARK 465 GLU A 329 REMARK 465 GLY A 330 REMARK 465 LYS A 331 REMARK 465 LYS A 370 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 GLU B 3 REMARK 465 SER B 4 REMARK 465 PRO B 5 REMARK 465 MET B 6 REMARK 465 PHE B 7 REMARK 465 ALA B 8 REMARK 465 ALA B 9 REMARK 465 ASN B 10 REMARK 465 GLY B 11 REMARK 465 MET B 12 REMARK 465 PRO B 13 REMARK 465 LYS B 14 REMARK 465 VAL B 15 REMARK 465 ASN B 16 REMARK 465 GLN B 17 REMARK 465 GLY B 18 REMARK 465 ALA B 19 REMARK 465 GLU B 20 REMARK 465 GLU B 21 REMARK 465 ASP B 22 REMARK 465 PRO B 327 REMARK 465 ALA B 328 REMARK 465 GLU B 329 REMARK 465 GLY B 330 REMARK 465 LYS B 331 REMARK 465 ALA B 332 REMARK 465 GLY B 333 REMARK 465 LEU B 334 REMARK 465 LYS B 370 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 B 2068 O HOH B 2158 1.79 REMARK 500 O HOH A 2109 O HOH A 2111 2.03 REMARK 500 O HOH A 2042 O HOH A 2112 2.08 REMARK 500 O HOH A 2042 O HOH A 2113 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 VAL A 198 CB VAL A 198 CG1 0.160 REMARK 500 VAL B 69 CB VAL B 69 CG1 0.138 REMARK 500 TYR B 167 CD1 TYR B 167 CE1 0.132 REMARK 500 PHE B 200 CZ PHE B 200 CE2 0.116 REMARK 500 TRP B 347 CB TRP B 347 CG -0.123 REMARK 500 GLU B 348 CD GLU B 348 OE1 0.076 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 29 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG A 53 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP A 352 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG A 365 NE - CZ - NH1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG A 365 NE - CZ - NH2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ARG B 24 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP B 29 CB - CG - OD2 ANGL. DEV. = 7.4 DEGREES REMARK 500 ASP B 80 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ARG B 142 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 LEU B 208 CB - CG - CD2 ANGL. DEV. = -19.9 DEGREES REMARK 500 ARG B 365 NE - CZ - NH1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ARG B 365 NE - CZ - NH2 ANGL. DEV. = -7.5 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 THR A 116 -77.43 -126.38 REMARK 500 ASP A 125 72.61 -152.98 REMARK 500 ASN A 129 24.48 -147.98 REMARK 500 LEU A 168 -12.57 -142.29 REMARK 500 SER A 195 34.76 -89.06 REMARK 500 HIS A 243 40.50 -107.01 REMARK 500 ASN A 256 40.83 -142.85 REMARK 500 HIS A 282 -127.98 51.49 REMARK 500 THR A 341 -120.59 -121.24 REMARK 500 THR B 116 -85.26 -130.16 REMARK 500 ASP B 125 73.52 -158.78 REMARK 500 ASN B 256 50.72 -140.27 REMARK 500 SER B 281 -157.84 -104.42 REMARK 500 HIS B 282 -132.75 47.48 REMARK 500 THR B 341 -118.34 -121.29 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 400 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 76 SG REMARK 620 2 HIS A 282 NE2 172.5 REMARK 620 3 GLU A 316 OE2 87.9 85.4 REMARK 620 4 ASP A 342 OD2 93.9 92.8 125.8 REMARK 620 5 HOH A2207 O 84.2 99.9 150.0 83.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 400 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 76 SG REMARK 620 2 HIS B 282 NE2 174.5 REMARK 620 3 GLU B 316 OE2 89.3 89.6 REMARK 620 4 ASP B 342 OD2 92.2 92.7 128.1 REMARK 620 5 HOH B2206 O 83.3 94.7 146.7 84.8 REMARK 620 N 1 2 3 4 REMARK 700 REMARK 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" REMARK 700 AND "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 8- REMARK 700 STRANDED BARRELS. THESE ARE REPRESENTED BY A 9-STRANDED SHEET IN REMARK 700 WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. 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 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEP A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEP B 508 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HFB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE TYROSINE-REGULATED 3-DEOXY-D-ARABINO- REMARK 900 HEPTULOSONATE-7-PHOSPHATE SYNTHASE FROM SACCHAROMYCES CEREVISIAE REMARK 900 COMPLEXED WITH PHOSPHOENOLPYRUVATE DBREF 1OAB A 1 370 UNP P32449 AROG_YEAST 1 370 DBREF 1OAB B 1 370 UNP P32449 AROG_YEAST 1 370 SEQRES 1 A 370 MET SER GLU SER PRO MET PHE ALA ALA ASN GLY MET PRO SEQRES 2 A 370 LYS VAL ASN GLN GLY ALA GLU GLU ASP VAL ARG ILE LEU SEQRES 3 A 370 GLY TYR ASP PRO LEU ALA SER PRO ALA LEU LEU GLN VAL SEQRES 4 A 370 GLN ILE PRO ALA THR PRO THR SER LEU GLU THR ALA LYS SEQRES 5 A 370 ARG GLY ARG ARG GLU ALA ILE ASP ILE ILE THR GLY LYS SEQRES 6 A 370 ASP ASP ARG VAL LEU VAL ILE VAL GLY PRO CYS SER ILE SEQRES 7 A 370 HIS ASP LEU GLU ALA ALA GLN GLU TYR ALA LEU ARG LEU SEQRES 8 A 370 LYS LYS LEU SER ASP GLU LEU LYS GLY ASP LEU SER ILE SEQRES 9 A 370 ILE MET ARG ALA TYR LEU GLU LYS PRO ARG THR THR VAL SEQRES 10 A 370 GLY TRP LYS GLY LEU ILE ASN ASP PRO ASP VAL ASN ASN SEQRES 11 A 370 THR PHE ASN ILE ASN LYS GLY LEU GLN SER ALA ARG GLN SEQRES 12 A 370 LEU PHE VAL ASN LEU THR ASN ILE GLY LEU PRO ILE GLY SEQRES 13 A 370 SER GLU MET LEU ASP THR ILE SER PRO GLN TYR LEU ALA SEQRES 14 A 370 ASP LEU VAL SER PHE GLY ALA ILE GLY ALA ARG THR THR SEQRES 15 A 370 GLU SER GLN LEU HIS ARG GLU LEU ALA SER GLY LEU SER SEQRES 16 A 370 PHE PRO VAL GLY PHE LYS ASN GLY THR ASP GLY THR LEU SEQRES 17 A 370 ASN VAL ALA VAL ASP ALA CYS GLN ALA ALA ALA HIS SER SEQRES 18 A 370 HIS HIS PHE MET GLY VAL THR LYS HIS GLY VAL ALA ALA SEQRES 19 A 370 ILE THR THR THR LYS GLY ASN GLU HIS CYS PHE VAL ILE SEQRES 20 A 370 LEU ARG GLY GLY LYS LYS GLY THR ASN TYR ASP ALA LYS SEQRES 21 A 370 SER VAL ALA GLU ALA LYS ALA GLN LEU PRO ALA GLY SER SEQRES 22 A 370 ASN GLY LEU MET ILE ASP TYR SER HIS GLY ASN SER ASN SEQRES 23 A 370 LYS ASP PHE ARG ASN GLN PRO LYS VAL ASN ASP VAL VAL SEQRES 24 A 370 CYS GLU GLN ILE ALA ASN GLY GLU ASN ALA ILE THR GLY SEQRES 25 A 370 VAL MET ILE GLU SER ASN ILE ASN GLU GLY ASN GLN GLY SEQRES 26 A 370 ILE PRO ALA GLU GLY LYS ALA GLY LEU LYS TYR GLY VAL SEQRES 27 A 370 SER ILE THR ASP ALA CYS ILE GLY TRP GLU THR THR GLU SEQRES 28 A 370 ASP VAL LEU ARG LYS LEU ALA ALA ALA VAL ARG GLN ARG SEQRES 29 A 370 ARG GLU VAL ASN LYS LYS SEQRES 1 B 370 MET SER GLU SER PRO MET PHE ALA ALA ASN GLY MET PRO SEQRES 2 B 370 LYS VAL ASN GLN GLY ALA GLU GLU ASP VAL ARG ILE LEU SEQRES 3 B 370 GLY TYR ASP PRO LEU ALA SER PRO ALA LEU LEU GLN VAL SEQRES 4 B 370 GLN ILE PRO ALA THR PRO THR SER LEU GLU THR ALA LYS SEQRES 5 B 370 ARG GLY ARG ARG GLU ALA ILE ASP ILE ILE THR GLY LYS SEQRES 6 B 370 ASP ASP ARG VAL LEU VAL ILE VAL GLY PRO CYS SER ILE SEQRES 7 B 370 HIS ASP LEU GLU ALA ALA GLN GLU TYR ALA LEU ARG LEU SEQRES 8 B 370 LYS LYS LEU SER ASP GLU LEU LYS GLY ASP LEU SER ILE SEQRES 9 B 370 ILE MET ARG ALA TYR LEU GLU LYS PRO ARG THR THR VAL SEQRES 10 B 370 GLY TRP LYS GLY LEU ILE ASN ASP PRO ASP VAL ASN ASN SEQRES 11 B 370 THR PHE ASN ILE ASN LYS GLY LEU GLN SER ALA ARG GLN SEQRES 12 B 370 LEU PHE VAL ASN LEU THR ASN ILE GLY LEU PRO ILE GLY SEQRES 13 B 370 SER GLU MET LEU ASP THR ILE SER PRO GLN TYR LEU ALA SEQRES 14 B 370 ASP LEU VAL SER PHE GLY ALA ILE GLY ALA ARG THR THR SEQRES 15 B 370 GLU SER GLN LEU HIS ARG GLU LEU ALA SER GLY LEU SER SEQRES 16 B 370 PHE PRO VAL GLY PHE LYS ASN GLY THR ASP GLY THR LEU SEQRES 17 B 370 ASN VAL ALA VAL ASP ALA CYS GLN ALA ALA ALA HIS SER SEQRES 18 B 370 HIS HIS PHE MET GLY VAL THR LYS HIS GLY VAL ALA ALA SEQRES 19 B 370 ILE THR THR THR LYS GLY ASN GLU HIS CYS PHE VAL ILE SEQRES 20 B 370 LEU ARG GLY GLY LYS LYS GLY THR ASN TYR ASP ALA LYS SEQRES 21 B 370 SER VAL ALA GLU ALA LYS ALA GLN LEU PRO ALA GLY SER SEQRES 22 B 370 ASN GLY LEU MET ILE ASP TYR SER HIS GLY ASN SER ASN SEQRES 23 B 370 LYS ASP PHE ARG ASN GLN PRO LYS VAL ASN ASP VAL VAL SEQRES 24 B 370 CYS GLU GLN ILE ALA ASN GLY GLU ASN ALA ILE THR GLY SEQRES 25 B 370 VAL MET ILE GLU SER ASN ILE ASN GLU GLY ASN GLN GLY SEQRES 26 B 370 ILE PRO ALA GLU GLY LYS ALA GLY LEU LYS TYR GLY VAL SEQRES 27 B 370 SER ILE THR ASP ALA CYS ILE GLY TRP GLU THR THR GLU SEQRES 28 B 370 ASP VAL LEU ARG LYS LEU ALA ALA ALA VAL ARG GLN ARG SEQRES 29 B 370 ARG GLU VAL ASN LYS LYS HET MN A 400 1 HET PEP A 508 10 HET MN B 400 1 HET PEP B 508 10 HETNAM MN MANGANESE (II) ION HETNAM PEP PHOSPHOENOLPYRUVATE FORMUL 3 MN 2(MN 2+) FORMUL 4 PEP 2(C3 H5 O6 P) FORMUL 7 HOH *417(H2 O) HELIX 1 1 SER A 33 ILE A 41 1 9 HELIX 2 2 THR A 44 THR A 63 1 20 HELIX 3 3 ASP A 80 LYS A 99 1 20 HELIX 4 4 ASN A 133 ASN A 150 1 18 HELIX 5 5 SER A 164 ALA A 169 1 6 HELIX 6 6 SER A 184 GLY A 193 1 10 HELIX 7 7 LEU A 208 ALA A 219 1 12 HELIX 8 8 ASP A 258 LEU A 269 1 12 HELIX 9 9 SER A 281 ASN A 286 5 6 HELIX 10 10 ASP A 288 ARG A 290 5 3 HELIX 11 11 ASN A 291 ASN A 305 1 15 HELIX 12 12 GLY A 346 LYS A 369 1 24 HELIX 13 13 SER B 33 ILE B 41 1 9 HELIX 14 14 THR B 44 THR B 63 1 20 HELIX 15 15 ASP B 80 LYS B 99 1 20 HELIX 16 16 ASN B 133 ASN B 150 1 18 HELIX 17 17 SER B 164 ALA B 169 1 6 HELIX 18 18 ASP B 170 VAL B 172 5 3 HELIX 19 19 SER B 184 GLY B 193 1 10 HELIX 20 20 LEU B 208 ALA B 219 1 12 HELIX 21 21 ASP B 258 LEU B 269 1 12 HELIX 22 22 SER B 281 ASN B 286 5 6 HELIX 23 23 ASP B 288 ARG B 290 5 3 HELIX 24 24 ASN B 291 ASN B 305 1 15 HELIX 25 25 GLY B 346 LYS B 369 1 24 SHEET 1 AA 3 ILE A 25 ASP A 29 0 SHEET 2 AA 3 ALA B 233 THR B 238 -1 O ILE B 235 N ASP A 29 SHEET 3 AA 3 HIS B 223 VAL B 227 -1 O PHE B 224 N THR B 236 SHEET 1 AB 9 VAL A 69 GLY A 74 0 SHEET 2 AB 9 LEU A 102 ARG A 107 1 O SER A 103 N VAL A 71 SHEET 3 AB 9 ILE A 155 GLU A 158 1 N GLY A 156 O MET A 106 SHEET 4 AB 9 VAL A 172 ILE A 177 1 N SER A 173 O ILE A 155 SHEET 5 AB 9 VAL A 198 LYS A 201 1 O GLY A 199 N ILE A 177 SHEET 6 AB 9 CYS A 244 LEU A 248 1 O PHE A 245 N PHE A 200 SHEET 7 AB 9 LEU A 276 ASP A 279 1 O MET A 277 N LEU A 248 SHEET 8 AB 9 ILE A 310 GLU A 316 1 N THR A 311 O LEU A 276 SHEET 9 AB 9 VAL A 69 GLY A 74 1 O LEU A 70 N VAL A 313 SHEET 1 AC 3 HIS A 223 VAL A 227 0 SHEET 2 AC 3 ALA A 233 THR A 238 -1 O ALA A 234 N GLY A 226 SHEET 3 AC 3 ILE B 25 ASP B 29 -1 N LEU B 26 O THR A 237 SHEET 1 BA 9 VAL B 69 GLY B 74 0 SHEET 2 BA 9 LEU B 102 ARG B 107 1 O SER B 103 N VAL B 71 SHEET 3 BA 9 ILE B 155 GLU B 158 1 N GLY B 156 O MET B 106 SHEET 4 BA 9 PHE B 174 ILE B 177 1 O PHE B 174 N SER B 157 SHEET 5 BA 9 VAL B 198 LYS B 201 1 O GLY B 199 N ILE B 177 SHEET 6 BA 9 CYS B 244 LEU B 248 1 O PHE B 245 N PHE B 200 SHEET 7 BA 9 LEU B 276 ASP B 279 1 O MET B 277 N LEU B 248 SHEET 8 BA 9 ILE B 310 GLU B 316 1 N THR B 311 O LEU B 276 SHEET 9 BA 9 VAL B 69 GLY B 74 1 O LEU B 70 N VAL B 313 LINK SG CYS A 76 MN MN A 400 1555 1555 2.61 LINK NE2 HIS A 282 MN MN A 400 1555 1555 2.25 LINK OE2 GLU A 316 MN MN A 400 1555 1555 1.97 LINK OD2 ASP A 342 MN MN A 400 1555 1555 2.17 LINK MN MN A 400 O HOH A2207 1555 1555 2.08 LINK SG CYS B 76 MN MN B 400 1555 1555 2.63 LINK NE2 HIS B 282 MN MN B 400 1555 1555 2.26 LINK OE2 GLU B 316 MN MN B 400 1555 1555 1.93 LINK OD2 ASP B 342 MN MN B 400 1555 1555 2.08 LINK MN MN B 400 O HOH B2206 1555 1555 2.15 SITE 1 AC1 6 CYS A 76 HIS A 282 GLU A 316 ASP A 342 SITE 2 AC1 6 PEP A 508 HOH A2207 SITE 1 AC2 6 CYS B 76 HIS B 282 GLU B 316 ASP B 342 SITE 2 AC2 6 PEP B 508 HOH B2206 SITE 1 AC3 15 ARG A 107 TYR A 109 LYS A 112 GLY A 178 SITE 2 AC3 15 ALA A 179 ARG A 180 LYS A 201 ARG A 249 SITE 3 AC3 15 HIS A 282 MN A 400 HOH A2052 HOH A2093 SITE 4 AC3 15 HOH A2207 HOH A2208 HOH A2209 SITE 1 AC4 14 ARG B 107 TYR B 109 LYS B 112 GLY B 178 SITE 2 AC4 14 ALA B 179 ARG B 180 LYS B 201 ARG B 249 SITE 3 AC4 14 HIS B 282 MN B 400 HOH B2053 HOH B2206 SITE 4 AC4 14 HOH B2207 HOH B2208 CRYST1 196.636 50.502 64.930 90.00 106.36 90.00 C 1 2 1 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 0.005085 0.000000 0.001493 0.00000 SCALE2 0.000000 0.019801 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016051 0.00000