HEADER PECTATE CLEAVAGE 24-APR-97 1AIR TITLE PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI (EC16) TO A TITLE 2 RESOLUTION OF 2.2 ANGSTROMS WITH 128 WATERS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PECTATE LYASE C; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PELC; COMPND 5 EC: 4.2.2.2 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ERWINIA CHRYSANTHEMI; SOURCE 3 ORGANISM_TAXID: 556; SOURCE 4 STRAIN: EC16; SOURCE 5 CELLULAR_LOCATION: EXTRACELLULAR; SOURCE 6 PLASMID: HB101 KEYWDS PECTATE CLEAVAGE, PECTINOLYITC ACTIVITY, TRANS-ELIMINATION EXPDTA X-RAY DIFFRACTION AUTHOR S.E.LIETZKE,R.D.SCAVETTA,M.D.YODER,F.A.JURNAK REVDAT 3 24-FEB-09 1AIR 1 VERSN REVDAT 2 01-APR-03 1AIR 1 JRNL REVDAT 1 16-JUN-97 1AIR 0 JRNL AUTH S.E.LIETZKE,R.D.SCAVETTA,M.D.YODER,F.JURNAK JRNL TITL THE REFINED THREE-DIMENSIONAL STRUCTURE OF PECTATE JRNL TITL 2 LYASE E FROM ERWINIA CHRYSANTHEMI AT 2.2 A JRNL TITL 3 RESOLUTION. JRNL REF PLANT PHYSIOL. V. 111 73 1996 JRNL REFN ISSN 0032-0889 JRNL PMID 12226275 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 25685 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 SET) : 0.172 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2642 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 128 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.77 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : 1.20 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1AIR COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : FEB-90 REMARK 200 TEMPERATURE (KELVIN) : 291 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : XUONG-HAMLIN MULTIWIRE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SDMS REMARK 200 DATA SCALING SOFTWARE : SDMS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25685 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.17500 REMARK 200 R SYM (I) : NULL 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 1.9 M REMARK 280 AMMONIUM SULFATE, 0.1M HEPES, PH 7.2 SYMMETRY OPERATIONS FOR REMARK 280 NON-STANDARD SETTING: SYMMETRY= (X,Y,Z) SYMMETRY=(-X+1/2,-Y,Z+ REMARK 280 1/2) SYMMETRY= (-X,Y+1/2,-Z+1/2) SYMMETRY=(X+1/2,-Y+1/2,-Z) 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 36.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.50000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.50000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.50000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.50000 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: MONOMERIC 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 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 LYS A 353 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 150 -139.12 -168.68 REMARK 500 ASP A 160 -0.04 68.57 REMARK 500 ASP A 162 13.46 -153.84 REMARK 500 ALA A 174 44.69 -80.95 REMARK 500 ARG A 203 158.17 80.79 REMARK 500 ASP A 214 69.32 66.62 REMARK 500 ARG A 218 73.89 65.83 REMARK 500 TYR A 268 -10.09 93.49 REMARK 500 ALA A 306 43.09 -90.87 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 SO4 A 1002 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1003 DBREF 1AIR A 1 353 UNP P11073 PELC_ERWCH 23 375 SEQRES 1 A 353 ALA THR ASP THR GLY GLY TYR ALA ALA THR ALA GLY GLY SEQRES 2 A 353 ASN VAL THR GLY ALA VAL SER LYS THR ALA THR SER MET SEQRES 3 A 353 GLN ASP ILE VAL ASN ILE ILE ASP ALA ALA ARG LEU ASP SEQRES 4 A 353 ALA ASN GLY LYS LYS VAL LYS GLY GLY ALA TYR PRO LEU SEQRES 5 A 353 VAL ILE THR TYR THR GLY ASN GLU ASP SER LEU ILE ASN SEQRES 6 A 353 ALA ALA ALA ALA ASN ILE CYS GLY GLN TRP SER LYS ASP SEQRES 7 A 353 PRO ARG GLY VAL GLU ILE LYS GLU PHE THR LYS GLY ILE SEQRES 8 A 353 THR ILE ILE GLY ALA ASN GLY SER SER ALA ASN PHE GLY SEQRES 9 A 353 ILE TRP ILE LYS LYS SER SER ASP VAL VAL VAL GLN ASN SEQRES 10 A 353 MET ARG ILE GLY TYR LEU PRO GLY GLY ALA LYS ASP GLY SEQRES 11 A 353 ASP MET ILE ARG VAL ASP ASP SER PRO ASN VAL TRP VAL SEQRES 12 A 353 ASP HIS ASN GLU LEU PHE ALA ALA ASN HIS GLU CYS ASP SEQRES 13 A 353 GLY THR PRO ASP ASN ASP THR THR PHE GLU SER ALA VAL SEQRES 14 A 353 ASP ILE LYS GLY ALA SER ASN THR VAL THR VAL SER TYR SEQRES 15 A 353 ASN TYR ILE HIS GLY VAL LYS LYS VAL GLY LEU ASP GLY SEQRES 16 A 353 SER SER SER SER ASP THR GLY ARG ASN ILE THR TYR HIS SEQRES 17 A 353 HIS ASN TYR TYR ASN ASP VAL ASN ALA ARG LEU PRO LEU SEQRES 18 A 353 GLN ARG GLY GLY LEU VAL HIS ALA TYR ASN ASN LEU TYR SEQRES 19 A 353 THR ASN ILE THR GLY SER GLY LEU ASN VAL ARG GLN ASN SEQRES 20 A 353 GLY GLN ALA LEU ILE GLU ASN ASN TRP PHE GLU LYS ALA SEQRES 21 A 353 ILE ASN PRO VAL THR SER ARG TYR ASP GLY LYS ASN PHE SEQRES 22 A 353 GLY THR TRP VAL LEU LYS GLY ASN ASN ILE THR LYS PRO SEQRES 23 A 353 ALA ASP PHE SER THR TYR SER ILE THR TRP THR ALA ASP SEQRES 24 A 353 THR LYS PRO TYR VAL ASN ALA ASP SER TRP THR SER THR SEQRES 25 A 353 GLY THR PHE PRO THR VAL ALA TYR ASN TYR SER PRO VAL SEQRES 26 A 353 SER ALA GLN CYS VAL LYS ASP LYS LEU PRO GLY TYR ALA SEQRES 27 A 353 GLY VAL GLY LYS ASN LEU ALA THR LEU THR SER THR ALA SEQRES 28 A 353 CYS LYS HET SO4 A1002 5 HET SO4 A1003 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *128(H2 O) HELIX 1 1 MET A 26 ALA A 35 1 10 HELIX 2 2 ASP A 61 ALA A 69 1 9 HELIX 3 3 ILE A 71 GLY A 73 5 3 HELIX 4 4 ASP A 288 THR A 291 1 4 HELIX 5 5 ALA A 327 LYS A 333 1 7 HELIX 6 6 PRO A 335 GLY A 336 5 2 HELIX 7 7 SER A 349 ALA A 351 5 3 SHEET 1 A10 VAL A 19 ALA A 23 0 SHEET 2 A10 LEU A 52 TYR A 56 1 SHEET 3 A10 ILE A 91 ILE A 94 1 SHEET 4 A10 VAL A 113 VAL A 114 1 SHEET 5 A10 VAL A 141 ASP A 144 1 SHEET 6 A10 THR A 177 SER A 181 1 SHEET 7 A10 ASN A 204 HIS A 208 1 SHEET 8 A10 LEU A 226 TYR A 230 1 SHEET 9 A10 GLN A 249 GLU A 253 1 SHEET 10 A10 THR A 275 LYS A 279 1 SHEET 1 B 9 GLY A 81 LYS A 85 0 SHEET 2 B 9 GLY A 104 LYS A 108 1 SHEET 3 B 9 ILE A 133 ASP A 136 1 SHEET 4 B 9 VAL A 169 LYS A 172 1 SHEET 5 B 9 LEU A 193 ASP A 194 1 SHEET 6 B 9 LEU A 221 ARG A 223 1 SHEET 7 B 9 LEU A 242 ARG A 245 1 SHEET 8 B 9 THR A 265 SER A 266 1 SHEET 9 B 9 VAL A 304 ASN A 305 -1 SHEET 1 C 6 ARG A 119 ILE A 120 0 SHEET 2 C 6 GLU A 147 PHE A 149 1 SHEET 3 C 6 TYR A 184 HIS A 186 1 SHEET 4 C 6 TYR A 211 ASN A 213 1 SHEET 5 C 6 LEU A 233 THR A 235 1 SHEET 6 C 6 TRP A 256 GLU A 258 1 SHEET 1 D 1 GLN A 249 THR A 295 0 SSBOND 1 CYS A 72 CYS A 155 1555 1555 2.02 SSBOND 2 CYS A 329 CYS A 352 1555 1555 2.03 CISPEP 1 LEU A 219 PRO A 220 0 0.27 SITE 1 AC1 3 ARG A 218 HOH A 412 HOH A 468 SITE 1 AC2 5 ARG A 218 LEU A 221 ARG A 245 HOH A 408 SITE 2 AC2 5 HOH A 468 CRYST1 72.000 83.000 95.000 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.013889 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012048 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010526 0.00000