HEADER TRANSFERASE/INHIBITOR 16-APR-23 8SIF TITLE CRYSTAL STRUCTURE OF ESCHERICHIA COLI HPPK IN COMPLEX WITH BISUBSTRATE TITLE 2 INHIBITOR HP-101 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-AMINO-4-HYDROXY-6-HYDROXYMETHYLDIHYDROPTERIDINE COMPND 3 PYROPHOSPHOKINASE; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE,PPPK,7, COMPND 6 8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE,HPPK; COMPND 7 EC: 2.7.6.3; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: FOLK, B0142, JW0138; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HPPK, BISUBSTRATE INHIBITOR, HP-101, TRANSFERASE, TRANSFERASE- KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR G.X.SHAW,G.SHI,X.JI REVDAT 1 03-JUL-24 8SIF 0 JRNL AUTH G.SHI,G.X.SHAW,X.JI JRNL TITL THE FIRST BISUBSTRATE INHIBITOR OF HPPK EXHIBITING CELL JRNL TITL 2 PERMEABILITY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 16055 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.070 REMARK 3 FREE R VALUE TEST SET COUNT : 975 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 29.4200 - 3.2500 0.93 2114 137 0.1377 0.1934 REMARK 3 2 3.2500 - 2.5800 0.98 2161 139 0.1770 0.2299 REMARK 3 3 2.5800 - 2.2500 0.99 2191 142 0.1916 0.2241 REMARK 3 4 2.2500 - 2.0500 0.99 2185 141 0.1831 0.2636 REMARK 3 5 2.0500 - 1.9000 0.96 2128 138 0.2207 0.2850 REMARK 3 6 1.9000 - 1.7900 0.98 2151 138 0.2404 0.3126 REMARK 3 7 1.7900 - 1.7000 0.98 2150 140 0.2957 0.3712 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.030 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 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 : 0.006 1460 REMARK 3 ANGLE : 0.797 2011 REMARK 3 CHIRALITY : 0.078 220 REMARK 3 PLANARITY : 0.007 266 REMARK 3 DIHEDRAL : 18.259 551 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 8SIF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-APR-23. REMARK 100 THE DEPOSITION ID IS D_1000273835. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-FEB-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16542 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.17600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 1.15000 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: FOURIER SYNTHESIS 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 (%): 41.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, NACL, PH 7.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 40.31250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.28800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.31250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.28800 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 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 0 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 86 -104.79 -134.25 REMARK 500 ALA A 86 -103.55 -134.25 REMARK 500 REMARK 500 REMARK: NULL DBREF 8SIF A 0 158 UNP P26281 HPPK_ECOLI 1 159 SEQRES 1 A 159 MET THR VAL ALA TYR ILE ALA ILE GLY SER ASN LEU ALA SEQRES 2 A 159 SER PRO LEU GLU GLN VAL ASN ALA ALA LEU LYS ALA LEU SEQRES 3 A 159 GLY ASP ILE PRO GLU SER HIS ILE LEU THR VAL SER SER SEQRES 4 A 159 PHE TYR ARG THR PRO PRO LEU GLY PRO GLN ASP GLN PRO SEQRES 5 A 159 ASP TYR LEU ASN ALA ALA VAL ALA LEU GLU THR SER LEU SEQRES 6 A 159 ALA PRO GLU GLU LEU LEU ASN HIS THR GLN ARG ILE GLU SEQRES 7 A 159 LEU GLN GLN GLY ARG VAL ARG LYS ALA GLU ARG TRP GLY SEQRES 8 A 159 PRO ARG THR LEU ASP LEU ASP ILE MET LEU PHE GLY ASN SEQRES 9 A 159 GLU VAL ILE ASN THR GLU ARG LEU THR VAL PRO HIS TYR SEQRES 10 A 159 ASP MET LYS ASN ARG GLY PHE MET LEU TRP PRO LEU PHE SEQRES 11 A 159 GLU ILE ALA PRO GLU LEU VAL PHE PRO ASP GLY GLU MET SEQRES 12 A 159 LEU ARG GLN ILE LEU HIS THR ARG ALA PHE ASP LYS LEU SEQRES 13 A 159 ASN LYS TRP HET ZX4 A 201 42 HETNAM ZX4 5'-S-{(2R,4R)-1-[3-(2-AMINO-4-OXO-4,7-DIHYDRO-3H- HETNAM 2 ZX4 PYRROLO[2,3-D]PYRIMIDIN-5-YL)PROPYL]-2- HETNAM 3 ZX4 CARBOXYPIPERIDIN-4-YL}-5'-THIOADENOSINE FORMUL 2 ZX4 C25 H32 N10 O6 S FORMUL 3 HOH *186(H2 O) HELIX 1 AA1 PRO A 14 ASP A 27 1 14 HELIX 2 AA2 ALA A 65 GLY A 81 1 17 HELIX 3 AA3 ASP A 117 ASN A 120 5 4 HELIX 4 AA4 ARG A 121 ALA A 132 1 12 HELIX 5 AA5 MET A 142 ALA A 151 1 10 SHEET 1 AA1 4 SER A 31 VAL A 36 0 SHEET 2 AA1 4 TYR A 53 THR A 62 -1 O ALA A 59 N LEU A 34 SHEET 3 AA1 4 VAL A 2 SER A 9 -1 N ALA A 3 O LEU A 60 SHEET 4 AA1 4 LEU A 94 PHE A 101 -1 O ASP A 97 N ALA A 6 SHEET 1 AA2 4 SER A 31 VAL A 36 0 SHEET 2 AA2 4 TYR A 53 THR A 62 -1 O ALA A 59 N LEU A 34 SHEET 3 AA2 4 TYR A 40 THR A 42 -1 N TYR A 40 O ASN A 55 SHEET 4 AA2 4 ASN A 156 LYS A 157 -1 O ASN A 156 N ARG A 41 SHEET 1 AA3 2 ILE A 106 ASN A 107 0 SHEET 2 AA3 2 THR A 112 VAL A 113 -1 O VAL A 113 N ILE A 106 CISPEP 1 VAL A 113 PRO A 114 0 -2.52 CRYST1 80.625 52.576 36.512 90.00 102.58 90.00 C 1 2 1 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 0.012403 0.000000 0.002768 0.00000 SCALE2 0.000000 0.019020 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028062 0.00000