HEADER LYASE 04-DEC-23 8RBR TITLE NEUTRON STRUCTURE OF ALGINATE LYASE PSPL7C FROM PARADENDRYPHIELLA TITLE 2 SALINA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALGINATE LYASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PARADENDRYPHIELLA SALINA; SOURCE 3 ORGANISM_TAXID: 179392; SOURCE 4 GENE: PSALG7C; SOURCE 5 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 4922 KEYWDS ALGINATE LYASE, NEUTRON STRUCTURE, BETA JELLY-ROLL, LYASE EXPDTA NEUTRON DIFFRACTION AUTHOR F.MEILLEUR,J.P.MORTH,C.WILKENS REVDAT 1 17-JAN-24 8RBR 0 JRNL AUTH F.MEILLEUR,J.P.MORTH,C.WILKENS JRNL TITL NEUTRON STRUCTURE OF ALGINATE LYASE PSPL7C FROM JRNL TITL 2 PARADENDRYPHIELLA SALINA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.23 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.080 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 41523 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.125 REMARK 3 FREE R VALUE : 0.167 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 2082 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.84 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2660 REMARK 3 BIN R VALUE (WORKING SET) : 0.1833 REMARK 3 BIN FREE R VALUE : 0.2070 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 120 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 : 1768 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 199 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.14 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.01 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) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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 8RBR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1292135111. REMARK 230 REMARK 230 EXPERIMENTAL DETAILS REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION REMARK 230 DATE OF DATA COLLECTION : 12-MAY-20 REMARK 230 TEMPERATURE (KELVIN) : 293.0 REMARK 230 PH : 4.00 REMARK 230 NUMBER OF CRYSTALS USED : 1 REMARK 230 REMARK 230 NEUTRON SOURCE : SPALLATION SOURCE REMARK 230 BEAMLINE : MANDI REMARK 230 WAVELENGTH OR RANGE (A) : 2-4 REMARK 230 MONOCHROMATOR : NULL REMARK 230 OPTICS : NULL REMARK 230 REMARK 230 DETECTOR TYPE : SCINTILLATION REMARK 230 DETECTOR MANUFACTURER : ORNL ANGER CAMERA REMARK 230 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 230 DATA SCALING SOFTWARE : NULL REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 41523 REMARK 230 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 230 RESOLUTION RANGE LOW (A) : 27.230 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 84.0 REMARK 230 DATA REDUNDANCY : 3.200 REMARK 230 R MERGE (I) : NULL REMARK 230 R SYM (I) : NULL REMARK 230 FOR THE DATA SET : 5.2900 REMARK 230 REMARK 230 IN THE HIGHEST RESOLUTION SHELL. REMARK 230 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 230 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 230 COMPLETENESS FOR SHELL (%) : NULL REMARK 230 DATA REDUNDANCY IN SHELL : NULL REMARK 230 R MERGE FOR SHELL (I) : NULL REMARK 230 R SYM FOR SHELL (I) : NULL REMARK 230 FOR SHELL : NULL REMARK 230 REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 230 SOFTWARE USED : NULL REMARK 230 STARTING MODEL: NULL REMARK 230 REMARK 230 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 1500; 0.1 M TBG BUFFER PH 4, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 20.78850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.65400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.48550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.65400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.78850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.48550 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 GLU A -1 REMARK 465 HIS A 247 REMARK 465 HIS A 248 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 D ILE A 150 D2 HOH A 342 3454 0.63 REMARK 500 D ILE A 150 O HOH A 342 3454 1.16 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 TRP A 37 138.36 -170.62 REMARK 500 THR A 39 -156.02 -121.44 REMARK 500 LYS A 64 -31.76 -142.12 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8RBR A 17 240 UNP A0A7I9C8Z1_9PLEO DBREF2 8RBR A A0A7I9C8Z1 17 240 SEQADV 8RBR GLU A -1 UNP A0A7I9C8Z EXPRESSION TAG SEQADV 8RBR PHE A 0 UNP A0A7I9C8Z EXPRESSION TAG SEQADV 8RBR VAL A 241 UNP A0A7I9C8Z EXPRESSION TAG SEQADV 8RBR ASP A 242 UNP A0A7I9C8Z EXPRESSION TAG SEQADV 8RBR HIS A 243 UNP A0A7I9C8Z EXPRESSION TAG SEQADV 8RBR HIS A 244 UNP A0A7I9C8Z EXPRESSION TAG SEQADV 8RBR HIS A 245 UNP A0A7I9C8Z EXPRESSION TAG SEQADV 8RBR HIS A 246 UNP A0A7I9C8Z EXPRESSION TAG SEQADV 8RBR HIS A 247 UNP A0A7I9C8Z EXPRESSION TAG SEQADV 8RBR HIS A 248 UNP A0A7I9C8Z EXPRESSION TAG SEQRES 1 A 234 GLU PHE LEU THR ALA VAL SER SER ILE ASP THR PHE LEU SEQRES 2 A 234 PRO VAL LEU ASN GLU ALA LYS LEU GLN TRP PRO THR SER SEQRES 3 A 234 ALA LEU ALA ALA SER SER GLU GLU LEU LEU GLY GLY TYR SEQRES 4 A 234 VAL GLY SER GLN PHE TYR LEU GLN ASP GLY LYS TYR MET SEQRES 5 A 234 GLN PHE GLN ILE ALA GLY SER SER ASN ARG CYS GLU LEU SEQRES 6 A 234 ARG GLN MET ILE PRO ASP GLY GLY SER GLU ILE GLY TRP SEQRES 7 A 234 ALA VAL ASP ASP GLY THR THR HIS THR ALA THR SER SER SEQRES 8 A 234 ILE VAL VAL PRO GLU GLN VAL ASP GLY VAL GLU GLU VAL SEQRES 9 A 234 THR ILE MET GLN ILE HIS SER GLY GLU ALA PRO GLN LEU SEQRES 10 A 234 ARG ILE SER TRP ILE ARG SER LYS SER LEU ASP GLY VAL SEQRES 11 A 234 ALA TYR GLU ASP PHE ILE MET SER THR VAL ARG ILE GLY SEQRES 12 A 234 THR GLY ASP SER SER ASP ASN PHE VAL LYS THR HIS LEU SEQRES 13 A 234 ALA ASP ARG THR ALA GLY ALA MET SER PHE GLN ILE ASP SEQRES 14 A 234 VAL LYS ASP SER LYS LEU THR ILE THR VAL ASN GLY ASN SEQRES 15 A 234 VAL VAL VAL ASN GLY GLN ASP LEU SER PHE TRP ASP GLY SEQRES 16 A 234 THR ASP SER CYS TYR PHE LYS ALA GLY ALA TYR ASN ASN SEQRES 17 A 234 ASN PRO THR SER GLU SER ALA THR ALA ARG ILE LYS PHE SEQRES 18 A 234 ALA ALA LEU ALA TRP VAL ASP HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *199(H2 O) HELIX 1 AA1 ALA A 19 ILE A 23 5 5 HELIX 2 AA2 PHE A 26 ASN A 31 1 6 HELIX 3 AA3 SER A 45 GLY A 51 1 7 HELIX 4 AA4 SER A 161 ASP A 163 5 3 HELIX 5 AA5 SER A 205 ASP A 208 5 4 SHEET 1 AA1 8 LEU A 42 ALA A 44 0 SHEET 2 AA1 8 ALA A 33 GLN A 36 -1 N LEU A 35 O ALA A 43 SHEET 3 AA1 8 ARG A 76 GLN A 81 -1 O GLU A 78 N GLN A 36 SHEET 4 AA1 8 TYR A 214 ASN A 221 -1 O ALA A 217 N LEU A 79 SHEET 5 AA1 8 GLU A 117 HIS A 124 -1 N THR A 119 O TYR A 220 SHEET 6 AA1 8 PRO A 129 LEU A 141 -1 O ILE A 133 N ILE A 120 SHEET 7 AA1 8 VAL A 144 ARG A 155 -1 O MET A 151 N SER A 134 SHEET 8 AA1 8 PHE A 165 ASP A 172 -1 O ALA A 171 N ILE A 150 SHEET 1 AA2 7 PHE A 58 GLN A 61 0 SHEET 2 AA2 7 TYR A 65 ALA A 71 -1 O TYR A 65 N GLN A 61 SHEET 3 AA2 7 THR A 230 ASP A 242 -1 O PHE A 235 N MET A 66 SHEET 4 AA2 7 HIS A 100 VAL A 107 -1 N VAL A 107 O LYS A 234 SHEET 5 AA2 7 MET A 178 LYS A 185 -1 O MET A 178 N ILE A 106 SHEET 6 AA2 7 LYS A 188 VAL A 193 -1 O THR A 192 N GLN A 181 SHEET 7 AA2 7 ASN A 196 ASP A 203 -1 O ASN A 196 N VAL A 193 CISPEP 1 TRP A 37 PRO A 38 0 -4.92 CRYST1 41.577 60.971 91.308 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 0.024052 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016401 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010952 0.00000