HEADER HYDROLASE 05-FEB-21 7E2A TITLE GDPD MUTANT FROM PYROCOCCUS FURIOSUS DSM 3638 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS DSM 3638; SOURCE 3 ORGANISM_TAXID: 186497; SOURCE 4 STRAIN: DSM 3638; SOURCE 5 GENE: PF2003; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GLYCEROPHOSPHATE PHOSPHODIESTERASE, HYDROLYSIS, KEYWDS 2 GLYCEROPHOSPHORYLCHOLINE, LYSOPHOSPHORYLCHOLINE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.H.WANG,J.WANG,F.H.WANG REVDAT 2 29-NOV-23 7E2A 1 REMARK REVDAT 1 09-FEB-22 7E2A 0 JRNL AUTH Y.H.WANG,J.WANG,F.H.WANG JRNL TITL CRYSTAL STRUCTURE OF GLYCEROPHOSHPHODIESTER PHOSPODIESTERASE JRNL TITL 2 D60A MUTANT FROM PYROCOCCUS FURIOSUS DSM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.08 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 18261 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 912 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 23.4500 - 3.9700 1.00 2618 140 0.1580 0.1862 REMARK 3 2 3.9700 - 3.1600 1.00 2503 116 0.1790 0.2237 REMARK 3 3 3.1600 - 2.7600 1.00 2470 133 0.2065 0.2830 REMARK 3 4 2.7600 - 2.5100 1.00 2465 124 0.2036 0.2833 REMARK 3 5 2.5100 - 2.3300 1.00 2429 136 0.2093 0.2408 REMARK 3 6 2.3300 - 2.1900 1.00 2432 129 0.2430 0.3001 REMARK 3 7 2.1900 - 2.0800 1.00 2432 134 0.2466 0.2952 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.214 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.564 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.85 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.98 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.014 2072 REMARK 3 ANGLE : 1.230 2794 REMARK 3 CHIRALITY : 0.065 320 REMARK 3 PLANARITY : 0.010 353 REMARK 3 DIHEDRAL : 6.059 274 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7E2A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1300020514. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-NOV-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97921 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AIMLESS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18312 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.080 REMARK 200 RESOLUTION RANGE LOW (A) : 23.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.90 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.08 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.13 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: PHASER REMARK 200 STARTING MODEL: 4OEC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES (PH 7.5), 25% W/V PEG3350, REMARK 280 0.2M AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 23.44500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.93500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.80000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.93500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.44500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.80000 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 MET A 1 REMARK 465 VAL A 2 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 LEU A 254 CG CD1 CD2 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 A 353 O HOH A 354 2.07 REMARK 500 REMARK 500 REMARK: NULL 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 O HOH A 361 O HOH A 362 3645 1.89 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 TYR A 20 66.92 -163.29 REMARK 500 MET A 58 137.57 -172.77 REMARK 500 LYS A 82 4.88 -66.41 REMARK 500 ASN A 129 81.05 69.93 REMARK 500 SER A 137 145.42 -175.81 REMARK 500 GLU A 223 54.45 30.87 REMARK 500 REMARK 500 REMARK: NULL DBREF 7E2A A 1 253 UNP Q8TZI9 Q8TZI9_PYRFU 1 253 SEQADV 7E2A ALA A 60 UNP Q8TZI9 ASP 60 ENGINEERED MUTATION SEQADV 7E2A LEU A 254 UNP Q8TZI9 EXPRESSION TAG SEQADV 7E2A GLU A 255 UNP Q8TZI9 EXPRESSION TAG SEQRES 1 A 255 MET VAL GLY ASN PRO MET TRP GLU ARG ASP LYS ILE ILE SEQRES 2 A 255 VAL LEU GLY HIS ARG GLY TYR MET ALA LYS TYR PRO GLU SEQRES 3 A 255 ASN SER LEU LEU SER ILE ARG LYS ALA ILE GLU ALA GLY SEQRES 4 A 255 ALA ASP GLY VAL GLU ILE ASP VAL TRP LEU SER LYS ASP SEQRES 5 A 255 ASN LYS VAL ILE LEU MET HIS ALA GLU THR ILE ASP ARG SEQRES 6 A 255 THR SER ASN LEU LYS GLY ARG GLN LYS GLU MET THR LEU SEQRES 7 A 255 GLU GLU LEU LYS LYS ALA ASN ILE GLY MET GLY GLU ARG SEQRES 8 A 255 ILE PRO THR LEU GLU GLU VAL PHE GLU ILE LEU PRO LYS SEQRES 9 A 255 ASP ALA LEU LEU ASN ILE GLU ILE LYS ASP ARG ASP ALA SEQRES 10 A 255 ALA LYS GLU VAL ALA ARG ILE VAL SER GLU ASN ASN PRO SEQRES 11 A 255 GLU ARG VAL MET ILE SER SER PHE ASP ILE GLU ALA LEU SEQRES 12 A 255 ARG GLU TYR ARG LYS TYR ASP ASP THR THR ILE MET GLY SEQRES 13 A 255 LEU LEU VAL ASP LYS GLU GLU THR VAL PRO LEU ILE PRO SEQRES 14 A 255 LYS LEU LYS GLU LYS LEU ASN LEU TRP SER VAL ASN VAL SEQRES 15 A 255 PRO MET GLU ALA ILE PRO ILE ILE GLY PHE GLU LYS THR SEQRES 16 A 255 TYR GLN ALA ILE LYS TRP VAL ARG SER LEU GLY LEU LYS SEQRES 17 A 255 ILE VAL LEU TRP THR GLU ASP ASP LYS LEU PHE TYR VAL SEQRES 18 A 255 ASP GLU ASN LEU LYS ARG LEU LEU GLY MET PHE GLU VAL SEQRES 19 A 255 VAL ILE ALA ASN ASP VAL GLU ARG MET VAL SER TYR LEU SEQRES 20 A 255 SER SER LEU GLY ILE ARG LEU GLU FORMUL 2 HOH *68(H2 O) HELIX 1 AA1 SER A 28 ALA A 38 1 11 HELIX 2 AA2 ARG A 72 MET A 76 5 5 HELIX 3 AA3 THR A 77 LYS A 82 1 6 HELIX 4 AA4 THR A 94 LEU A 102 1 9 HELIX 5 AA5 ASP A 114 ASP A 116 5 3 HELIX 6 AA6 ALA A 117 ASN A 128 1 12 HELIX 7 AA7 ASN A 129 GLU A 131 5 3 HELIX 8 AA8 ASP A 139 ASP A 150 1 12 HELIX 9 AA9 LYS A 161 PRO A 166 5 6 HELIX 10 AB1 LEU A 167 ASN A 176 1 10 HELIX 11 AB2 GLU A 185 GLY A 191 1 7 HELIX 12 AB3 GLY A 191 LEU A 205 1 15 HELIX 13 AB4 ASP A 216 VAL A 221 1 6 HELIX 14 AB5 GLU A 223 LEU A 228 1 6 HELIX 15 AB6 ASP A 239 LEU A 250 1 12 SHEET 1 AA110 VAL A 55 LEU A 57 0 SHEET 2 AA110 GLY A 42 LEU A 49 -1 N TRP A 48 O ILE A 56 SHEET 3 AA110 LEU A 107 ILE A 112 1 O GLU A 111 N ILE A 45 SHEET 4 AA110 VAL A 133 SER A 137 1 O MET A 134 N ILE A 110 SHEET 5 AA110 ILE A 154 LEU A 158 1 O GLY A 156 N ILE A 135 SHEET 6 AA110 SER A 179 PRO A 183 1 O ASN A 181 N LEU A 157 SHEET 7 AA110 LYS A 208 TRP A 212 1 O VAL A 210 N VAL A 182 SHEET 8 AA110 VAL A 234 ALA A 237 1 O ILE A 236 N LEU A 211 SHEET 9 AA110 ILE A 13 GLY A 16 1 N LEU A 15 O ALA A 237 SHEET 10 AA110 GLY A 42 LEU A 49 1 O GLU A 44 N GLY A 16 CRYST1 46.890 69.600 89.870 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 0.021327 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014368 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011127 0.00000