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Basic information

Entry
Database: PDB / ID: 4uma
TitleStructural analysis of substrate-mimicking inhibitors in complex with Neisseria meningitidis 3 deoxy D arabino heptulosonate 7 phosphate synthase the importance of accommodating the active site water
ComponentsPHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
KeywordsTRANSFERASE / DAH7PS / DAHPS / AROMATIC AMINO ACIDS / SHIKIMATE PATHWAY / OXOCARBENIUM ION / ENZYME INHIBITORS / MENINGITIS
Function / homology
Function and homology information


3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / metal ion binding / identical protein binding / cytoplasm
Similarity search - Function
DAHP synthase, class 1 / DAHP synthetase I/KDSA / DAHP synthetase I family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
(E)-2-METHYL-3-PHOSPHONOACRYLATE / : / Phospho-2-dehydro-3-deoxyheptonate aldolase
Similarity search - Component
Biological speciesNEISSERIA MENINGITIDIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.76 Å
AuthorsHeyes, L.C. / Reichau, S. / Cross, P.J. / Parker, E.J.
CitationJournal: Bioorg.Chem. / Year: 2014
Title: Structural Analysis of Substrate-Mimicking Inhibitors in Complex with Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase - the Importance of Accommodating the Active Site Water.
Authors: Heyes, L.C. / Reichau, S. / Cross, P.J. / Jameson, G.B. / Parker, E.J.
History
DepositionMay 16, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Apr 6, 2016Group: Data collection
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
B: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
C: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
D: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,73312
Polymers154,8494
Non-polymers8848
Water14,034779
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10180 Å2
ΔGint-45 kcal/mol
Surface area43490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.495, 136.501, 76.157
Angle α, β, γ (deg.)90.00, 96.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE / 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE / DAHP SYNTHASE / PHOSPHO-2-KETO-3- ...3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE / DAHP SYNTHASE / PHOSPHO-2-KETO-3-DEOXYHEPTONATE ALDOLASE


Mass: 38712.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEISSERIA MENINGITIDIS (bacteria) / Strain: MC58 / Plasmid: PT7/7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9K169, 3-deoxy-7-phosphoheptulonate synthase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-GZ3 / (E)-2-METHYL-3-PHOSPHONOACRYLATE


Mass: 166.069 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H7O5P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 779 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.78 % / Description: NONE
Crystal growpH: 7.3 / Details: pH 7.3

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Data collection

DiffractionMean temperature: 153 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1.3
DetectorType: ADSC CCD / Detector: CCD / Date: May 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 1.76→46.82 Å / Num. obs: 147006 / % possible obs: 99.8 % / Observed criterion σ(I): 1.9 / Redundancy: 7.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.9
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 1.9 / % possible all: 99.2

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 4HSN

4hsn


Resolution: 1.76→73.04 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 6.409 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 7367 5 %RANDOM
Rwork0.19061 ---
obs0.19181 139178 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20.15 Å2
2---0.06 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.76→73.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10103 0 44 779 10926
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01910386
X-RAY DIFFRACTIONr_bond_other_d0.0060.029896
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.96114087
X-RAY DIFFRACTIONr_angle_other_deg1.06322710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.01551342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.06323.898449
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13151731
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6071571
X-RAY DIFFRACTIONr_chiral_restr0.080.21590
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02111913
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.991.775356
X-RAY DIFFRACTIONr_mcbond_other0.991.775355
X-RAY DIFFRACTIONr_mcangle_it1.4082.6516696
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4951.9425030
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 522 -
Rwork0.304 10225 -
obs--99.2 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.81360.0034-0.24910.7179-0.25760.6602-0.12280.1743-0.3616-0.06080.0104-0.07960.14990.03630.11240.052-0.01420.03010.0383-0.02370.0917-3.252-86.787-7.624
22.1109-0.0643-0.22980.5368-0.13710.7955-0.0534-0.04890.13540.05380.0820.06580.0006-0.1356-0.02860.0109-0.0046-0.00510.07380.01270.0768-34.898-73.7770.369
31.61310.38830.20291.7736-0.68810.89390.0402-0.02530.07720.0635-0.1-0.1427-0.1020.10510.05980.0183-0.0307-0.0060.13910.08350.11024.763-36.932-30.58
41.68940.20350.42041.086-0.41140.91690.02140.18090.0931-0.20480.13160.34620.0895-0.0406-0.1530.0494-0.0265-0.07170.16270.15460.2418-26.692-43.035-45.159
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 349
2X-RAY DIFFRACTION2B17 - 349
3X-RAY DIFFRACTION3C16 - 349
4X-RAY DIFFRACTION4D16 - 349

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