HEADER LYASE 13-MAY-99 1QCX TITLE PECTIN LYASE B COMPND MOL_ID: 1; COMPND 2 MOLECULE: PECTIN LYASE B; COMPND 3 CHAIN: A; COMPND 4 EC: 4.2.2.10 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ASPERGILLUS NIGER; SOURCE 3 ORGANISM_TAXID: 5061 KEYWDS PECTIN LYASE, BETA-HELIX PROTEIN, PECTIN, PLANT CELL WALL, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR J.VITALI,F.JURNAK REVDAT 4 03-APR-24 1QCX 1 SEQADV REVDAT 3 24-FEB-09 1QCX 1 VERSN REVDAT 2 01-APR-03 1QCX 1 JRNL REVDAT 1 19-MAY-99 1QCX 0 JRNL AUTH J.VITALI,B.SCHICK,H.C.KESTER,J.VISSER,F.JURNAK JRNL TITL THE TREE-DIMENSIONAL STRUCTURE OF ASPERGILLUS NIGER PECTIN JRNL TITL 2 LYASE B AT 1.7-A RESOLUTION. JRNL REF PLANT PHYSIOL. V. 116 69 1998 JRNL REFN ISSN 0032-0889 JRNL PMID 9449837 JRNL DOI 10.1104/PP.116.1.69 REMARK 2 REMARK 2 RESOLUTION. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.1000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.8 REMARK 3 NUMBER OF REFLECTIONS : 32007 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : R-FREE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3204 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.78 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.87 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3462 REMARK 3 BIN R VALUE (WORKING SET) : 0.2040 REMARK 3 BIN FREE R VALUE : 0.2190 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 411 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2662 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 339 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.50 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) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 2.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : 1.400 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) : 1.300 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.000 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 2.900 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.500 ; 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: FREE R WAS USED UNTIL LAST CYCLE WHEN REMARK 3 ALL DATA WAS INCLUDED REMARK 4 REMARK 4 1QCX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000175905. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 295.0 REMARK 200 PH : 5.0 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 RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : XUONG-HAMLIN MULTIWIRE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SDMS SOFTWARE PACKAGE REMARK 200 DATA SCALING SOFTWARE : SDMS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50124 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 73.8 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05400 REMARK 200 FOR THE DATA SET : 18.9000 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 AND REMARK 200 HEAVY ATOMS REMARK 200 SOFTWARE USED: PHASES, HEAVY, X-PLOR 3.1 REMARK 200 STARTING MODEL: FOR MOLECULAR REPLACEMENT: PARALLEL BETA HELIX OF REMARK 200 PELE, ALL AMINO ACIDS REPLACED WITH ALA UNLESS COMMON IN THE TWO REMARK 200 PROTEINS; HEAVY ATOMS: PT, HG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 41.85000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.40000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 41.85000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.40000 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 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 MET A 237 CG MET A 237 SD 0.198 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 HIS A 79 52.96 39.41 REMARK 500 ASN A 134 66.38 62.92 REMARK 500 ASN A 146 62.48 38.12 REMARK 500 TRP A 151 8.54 83.07 REMARK 500 ASP A 160 83.77 75.77 REMARK 500 SER A 161 -166.89 -160.95 REMARK 500 ARG A 176 -123.09 -121.97 REMARK 500 ASN A 187 -124.64 49.03 REMARK 500 TRP A 212 79.53 -100.36 REMARK 500 ASN A 220 73.04 -167.46 REMARK 500 ARG A 236 58.21 37.68 REMARK 500 GLN A 241 -169.92 -166.49 REMARK 500 ASN A 243 71.21 -158.80 REMARK 500 ALA A 260 -87.61 -104.78 REMARK 500 REMARK 500 REMARK: NULL DBREF 1QCX A 1 359 UNP Q00205 PLYB_ASPNG 21 378 SEQADV 1QCX GLN A 47 UNP Q00205 ARG 67 SEE REMARK 999 SEQADV 1QCX TYR A 96 UNP Q00205 INSERTION SEQADV 1QCX VAL A 281 UNP Q00205 ILE 300 SEE REMARK 999 SEQADV 1QCX ALA A 346 UNP Q00205 ASN 365 SEE REMARK 999 SEQRES 1 A 359 ALA GLY VAL VAL GLY ALA ALA GLU GLY PHE ALA HIS GLY SEQRES 2 A 359 VAL THR GLY GLY GLY SER ALA SER PRO VAL TYR PRO THR SEQRES 3 A 359 THR THR ASP GLU LEU VAL SER TYR LEU GLY ASP ASN GLU SEQRES 4 A 359 PRO ARG VAL ILE ILE LEU ASP GLN THR PHE ASP PHE THR SEQRES 5 A 359 GLY THR GLU GLY THR GLU THR THR THR GLY CYS ALA PRO SEQRES 6 A 359 TRP GLY THR ALA SER GLN CYS GLN VAL ALA ILE ASN LEU SEQRES 7 A 359 HIS SER TRP CYS ASP ASN TYR GLN ALA SER ALA PRO LYS SEQRES 8 A 359 VAL SER VAL THR TYR ASP LYS ALA GLY ILE LEU PRO ILE SEQRES 9 A 359 THR VAL ASN SER ASN LYS SER ILE VAL GLY GLN GLY THR SEQRES 10 A 359 LYS GLY VAL ILE LYS GLY LYS GLY LEU ARG VAL VAL SER SEQRES 11 A 359 GLY ALA LYS ASN VAL ILE ILE GLN ASN ILE ALA VAL THR SEQRES 12 A 359 ASP ILE ASN PRO LYS TYR VAL TRP GLY GLY ASP ALA ILE SEQRES 13 A 359 THR VAL ASP ASP SER ASP LEU VAL TRP ILE ASP HIS VAL SEQRES 14 A 359 THR THR ALA ARG ILE GLY ARG GLN HIS ILE VAL LEU GLY SEQRES 15 A 359 THR SER ALA ASP ASN ARG VAL THR ILE SER TYR SER LEU SEQRES 16 A 359 ILE ASP GLY ARG SER ASP TYR SER ALA THR CYS ASN GLY SEQRES 17 A 359 HIS HIS TYR TRP GLY VAL TYR LEU ASP GLY SER ASN ASP SEQRES 18 A 359 MET VAL THR LEU LYS GLY ASN TYR PHE TYR ASN LEU SER SEQRES 19 A 359 GLY ARG MET PRO LYS VAL GLN GLY ASN THR LEU LEU HIS SEQRES 20 A 359 ALA VAL ASN ASN LEU PHE HIS ASN PHE ASP GLY HIS ALA SEQRES 21 A 359 PHE GLU ILE GLY THR GLY GLY TYR VAL LEU ALA GLU GLY SEQRES 22 A 359 ASN VAL PHE GLN ASP VAL ASN VAL VAL VAL GLU THR PRO SEQRES 23 A 359 ILE SER GLY GLN LEU PHE SER SER PRO ASP ALA ASN THR SEQRES 24 A 359 ASN GLN GLN CYS ALA SER VAL PHE GLY ARG SER CYS GLN SEQRES 25 A 359 LEU ASN ALA PHE GLY ASN SER GLY SER MET SER GLY SER SEQRES 26 A 359 ASP THR SER ILE ILE SER LYS PHE ALA GLY LYS THR ILE SEQRES 27 A 359 ALA ALA ALA HIS PRO PRO GLY ALA ILE ALA GLN TRP THR SEQRES 28 A 359 MET LYS ASN ALA GLY GLN GLY LYS FORMUL 2 HOH *339(H2 O) HELIX 1 A THR A 28 GLY A 36 1 9 HELIX 2 B TRP A 81 ASN A 84 1 4 HELIX 3 C LYS A 98 ILE A 101 5 4 HELIX 4 D ASN A 298 CYS A 303 5 6 HELIX 5 D' ALA A 304 PHE A 307 1 4 HELIX 6 E THR A 327 PHE A 333 5 7 HELIX 7 F PRO A 344 ALA A 346 5 3 HELIX 8 F' ILE A 347 ASN A 354 1 8 SHEET 1 PB1 7 ILE A 104 THR A 105 0 SHEET 2 PB1 7 LEU A 126 VAL A 128 1 SHEET 3 PB1 7 ILE A 156 VAL A 158 1 SHEET 4 PB1 7 ILE A 179 LEU A 181 1 SHEET 5 PB1 7 VAL A 214 LEU A 216 1 SHEET 6 PB1 7 LYS A 239 VAL A 240 1 SHEET 7 PB1 7 GLU A 262 ILE A 263 1 SHEET 1 PB2 9 ARG A 41 LEU A 45 0 SHEET 2 PB2 9 LYS A 110 GLY A 114 1 SHEET 3 PB2 9 VAL A 135 GLN A 138 1 SHEET 4 PB2 9 ILE A 104 ASN A 107 1 SHEET 5 PB2 9 VAL A 189 SER A 192 1 SHEET 6 PB2 9 ASP A 221 LYS A 226 1 SHEET 7 PB2 9 THR A 244 VAL A 249 1 SHEET 8 PB2 9 GLY A 267 GLU A 272 1 SHEET 9 PB2 9 GLN A 290 PHE A 292 1 SHEET 1 PB3 9 THR A 48 ASP A 50 0 SHEET 2 PB3 9 VAL A 120 LYS A 122 1 SHEET 3 PB3 9 ALA A 141 THR A 143 1 SHEET 4 PB3 9 THR A 170 THR A 171 1 SHEET 5 PB3 9 LEU A 195 ASP A 197 1 SHEET 6 PB3 9 TYR A 229 TYR A 231 1 SHEET 7 PB3 9 LEU A 252 HIS A 254 1 SHEET 8 PB3 9 VAL A 275 GLN A 277 1 SHEET 9 PB3 9 ALA A 315 GLY A 317 1 SHEET 1 J 4 LYS A 91 TYR A 96 0 SHEET 2 J 4 THR A 57 CYS A 63 1 SHEET 3 J 4 VAL A 74 ILE A 76 1 SHEET 4 J 4 TYR A 149 VAL A 150 1 SSBOND 1 CYS A 63 CYS A 82 1555 1555 2.03 SSBOND 2 CYS A 72 CYS A 206 1555 1555 2.03 SSBOND 3 CYS A 303 CYS A 311 1555 1555 2.03 CISPEP 1 GLY A 182 THR A 183 0 0.47 CISPEP 2 MET A 237 PRO A 238 0 -0.38 CISPEP 3 THR A 285 PRO A 286 0 -1.04 CRYST1 83.700 88.800 42.284 90.00 90.00 90.00 P 21 21 2 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 0.011947 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011261 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023650 0.00000