HEADER TRANSFERASE 28-FEB-19 6QUR TITLE MAPPING THE ALLOSTERIC COMMUNICATION NETWORK OF AMINODEOXYCHORISMATE TITLE 2 SYNTHASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMINASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ALLOSTERY, ANCESTRAL SEQUENCE RECONSTRUCTION, CATALYTIC TRIAD, KEYWDS 2 GLUTAMINE AMIDOTRANSFERASES, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR F.SEMMELMANN,K.STRAUB,C.RAJENDRAN,J.NAZET REVDAT 3 25-SEP-19 6QUR 1 REMARK REVDAT 2 10-JUL-19 6QUR 1 JRNL REVDAT 1 05-JUN-19 6QUR 0 JRNL AUTH F.SEMMELMANN,K.STRAUB,J.NAZET,C.RAJENDRAN,R.MERKL,R.STERNER JRNL TITL MAPPING THE ALLOSTERIC COMMUNICATION NETWORK OF JRNL TITL 2 AMINODEOXYCHORISMATE SYNTHASE. JRNL REF J.MOL.BIOL. V. 431 2718 2019 JRNL REFN ESSN 1089-8638 JRNL PMID 31121180 JRNL DOI 10.1016/J.JMB.2019.05.021 REMARK 2 REMARK 2 RESOLUTION. 1.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.73 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 19366 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 969 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 45.2608 - 3.4281 1.00 2773 146 0.1807 0.2237 REMARK 3 2 3.4281 - 2.7211 1.00 2670 140 0.2239 0.3163 REMARK 3 3 2.7211 - 2.3771 1.00 2611 138 0.2436 0.2803 REMARK 3 4 2.3771 - 2.1598 1.00 2604 138 0.2462 0.2719 REMARK 3 5 2.1598 - 2.0050 1.00 2593 136 0.2411 0.2884 REMARK 3 6 2.0050 - 1.8868 1.00 2567 135 0.2699 0.3205 REMARK 3 7 1.8868 - 1.7923 0.99 2579 136 0.3197 0.3533 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.890 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.96 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 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 : 0.007 1554 REMARK 3 ANGLE : 0.886 2105 REMARK 3 CHIRALITY : 0.058 237 REMARK 3 PLANARITY : 0.005 271 REMARK 3 DIHEDRAL : 3.084 926 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 6QUR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-FEB-19. REMARK 100 THE DEPOSITION ID IS D_1292100901. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUL-17 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 : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19372 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.792 REMARK 200 RESOLUTION RANGE LOW (A) : 39.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.00 REMARK 200 R MERGE (I) : 0.06472 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.5200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 11.80 REMARK 200 R MERGE FOR SHELL (I) : 1.93500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.270 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG, VAPOR DIFFUSION, TEMPERATURE 291K 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 23.87750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.79150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.19500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.79150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.87750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.19500 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: 9110 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 HIS A 194 REMARK 465 HIS A 195 REMARK 465 HIS A 196 REMARK 465 HIS A 197 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 GLU A 58 CG CD OE1 OE2 REMARK 470 ASP A 150 CG OD1 OD2 REMARK 470 GLU A 191 CG CD OE1 OE2 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 OE2 GLU A 172 O HOH A 201 2.10 REMARK 500 O HOH A 262 O HOH A 287 2.10 REMARK 500 O HOH A 294 O HOH A 305 2.16 REMARK 500 O HOH A 286 O HOH A 298 2.18 REMARK 500 O HOH A 206 O HOH A 303 2.18 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 CYS A 79 -131.96 54.15 REMARK 500 ASP A 150 -146.59 64.21 REMARK 500 REMARK 500 REMARK: NULL DBREF 6QUR A 1 197 PDB 6QUR 6QUR 1 197 SEQRES 1 A 197 MET ILE LEU MET ILE ASP ASN TYR ASP SER PHE THR TYR SEQRES 2 A 197 ASN LEU VAL GLN TYR LEU GLY GLU LEU GLY GLU GLU VAL SEQRES 3 A 197 VAL VAL TYR ARG ASN ASP GLU ILE THR ILE ALA GLU ILE SEQRES 4 A 197 GLU LYS LEU LYS PRO ASP HIS LEU VAL ILE SER PRO GLY SEQRES 5 A 197 PRO CYS THR PRO ASN GLU ALA GLY ILE SER LEU GLU VAL SEQRES 6 A 197 ILE LYS HIS PHE ALA GLY LYS ILE PRO ILE LEU GLY VAL SEQRES 7 A 197 CYS LEU GLY HIS GLN SER ILE GLY GLN ALA PHE GLY GLY SEQRES 8 A 197 LYS ILE VAL ARG ALA LYS GLN VAL MET HIS GLY LYS THR SEQRES 9 A 197 SER GLU ILE TYR HIS ASN ASN LYS GLY VAL PHE LYS GLY SEQRES 10 A 197 LEU ASN ASN PRO PHE GLU ALA THR ARG TYR HIS SER LEU SEQRES 11 A 197 VAL VAL GLU ARG GLU THR LEU PRO ASP CYS LEU GLU ILE SEQRES 12 A 197 THR ALA TRP THR GLU THR ASP GLU GLY GLU ILE MET GLY SEQRES 13 A 197 ILE ARG HIS LYS THR LEU PRO ILE GLU GLY VAL GLN PHE SEQRES 14 A 197 HIS PRO GLU SER ILE LEU THR GLU GLN GLY HIS GLU LEU SEQRES 15 A 197 LEU LYS ASN PHE LEU LYS GLU LEU GLU HIS HIS HIS HIS SEQRES 16 A 197 HIS HIS FORMUL 2 HOH *113(H2 O) HELIX 1 AA1 PHE A 11 LEU A 22 1 12 HELIX 2 AA2 ASP A 32 ILE A 34 5 3 HELIX 3 AA3 THR A 35 LYS A 43 1 9 HELIX 4 AA4 SER A 62 ALA A 70 1 9 HELIX 5 AA5 LEU A 80 PHE A 89 1 10 HELIX 6 AA6 LYS A 112 LYS A 116 5 5 HELIX 7 AA7 HIS A 170 LEU A 175 5 6 HELIX 8 AA8 THR A 176 GLU A 189 1 14 SHEET 1 AA1 9 VAL A 26 ARG A 30 0 SHEET 2 AA1 9 ILE A 2 ASP A 6 1 N MET A 4 O VAL A 27 SHEET 3 AA1 9 HIS A 46 ILE A 49 1 O VAL A 48 N ILE A 5 SHEET 4 AA1 9 ILE A 75 GLY A 77 1 O LEU A 76 N ILE A 49 SHEET 5 AA1 9 ILE A 164 VAL A 167 1 O GLU A 165 N GLY A 77 SHEET 6 AA1 9 ILE A 154 HIS A 159 -1 N ILE A 157 O GLY A 166 SHEET 7 AA1 9 LEU A 141 TRP A 146 -1 N ALA A 145 O MET A 155 SHEET 8 AA1 9 THR A 104 HIS A 109 -1 N TYR A 108 O TRP A 146 SHEET 9 AA1 9 PHE A 122 THR A 125 -1 O PHE A 122 N ILE A 107 SHEET 1 AA2 2 ILE A 93 VAL A 94 0 SHEET 2 AA2 2 VAL A 131 VAL A 132 -1 O VAL A 131 N VAL A 94 SSBOND 1 CYS A 54 CYS A 79 1555 1555 2.05 CISPEP 1 GLY A 52 PRO A 53 0 2.30 CISPEP 2 ASN A 120 PRO A 121 0 5.37 CRYST1 47.755 58.390 71.583 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 0.020940 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017126 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013970 0.00000