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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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