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- PDB-5cz0: Neisseria meningitidis 3 dexy-D-arabino-heptulosonate 7-phosphate... -

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Basic information

Entry
Database: PDB / ID: 5cz0
TitleNeisseria meningitidis 3 dexy-D-arabino-heptulosonate 7-phosphate synthase Glu98Ala variant
ComponentsPhospho-2-dehydro-3-deoxyheptonate aldolase
KeywordsTRANSFERASE / NmeDAH7PS / Substrate
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 / 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
: / PHOSPHOENOLPYRUVATE / Phospho-2-dehydro-3-deoxyheptonate aldolase
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHeyes, L.C. / Parker, E.J.
CitationJournal: To Be Published
Title: NmeDAH7PS E98A variant at 2.5 Angstroms resolution
Authors: Heyes, L.C. / Parker, E.J.
History
DepositionJul 31, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)155,82516
Polymers154,6164
Non-polymers1,20812
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12420 Å2
ΔGint-108 kcal/mol
Surface area43750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.850, 135.250, 76.040
Angle α, β, γ (deg.)90.00, 95.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#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: 38654.102 Da / Num. of mol.: 4 / Mutation: E98A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (strain MC58) (bacteria)
Strain: MC58 / Gene: aroG, NMB0307 / Plasmid: pT7-7 / Cell line (production host): BL21* / Production host: Escherichia coli (E. coli)
References: UniProt: Q9K169, 3-deoxy-7-phosphoheptulonate synthase

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Non-polymers , 5 types, 124 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-PEP / PHOSPHOENOLPYRUVATE


Mass: 168.042 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5O6P
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.65 % / Description: Monoclinic, P1211
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.1M Tris HCl (pH 7.3), 0.2 M trimethyl-amino-N-oxide (TMAO), 0.4 mM MnSO4 and PEG 2000MME

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.5→75.63 Å / Num. obs: 50068 / % possible obs: 97.7 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.122 / Net I/av σ(I): 9 / Net I/σ(I): 9
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.753 / Mean I/σ(I) obs: 2 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HSN

4hsn


Resolution: 2.5→75.63 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.906 / SU B: 25.714 / SU ML: 0.261 / Cross valid method: FREE R-VALUE / ESU R: 0.661 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26394 3103 6.2 %4HSN
Rwork0.20031 ---
obs0.20438 46903 97.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.792 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å20.54 Å2
2--2.7 Å20 Å2
3----1.75 Å2
Refinement stepCycle: 1 / Resolution: 2.5→75.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9978 0 62 112 10152
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01910244
X-RAY DIFFRACTIONr_bond_other_d0.0010.029682
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.96113910
X-RAY DIFFRACTIONr_angle_other_deg0.82322172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.46651330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73523.867437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.945151645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7861568
X-RAY DIFFRACTIONr_chiral_restr0.0740.21578
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111789
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022311
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_it1.8143.0855323
X-RAY DIFFRACTIONr_mcbond_other1.8133.0845322
X-RAY DIFFRACTIONr_mcangle_it3.0194.626649
X-RAY DIFFRACTIONr_mcangle_other3.0194.626650
X-RAY DIFFRACTIONr_scbond_it1.8223.244921
X-RAY DIFFRACTIONr_scbond_other1.8223.244922
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9984.7997261
X-RAY DIFFRACTIONr_long_range_B_refined5.0124.43411335
X-RAY DIFFRACTIONr_long_range_B_other5.0124.43711336
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 192 -
Rwork0.31 3475 -
obs--97.06 %
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)
11.3641-0.191-0.22120.67940.58050.5075-0.0755-0.0139-0.1240.1718-0.02950.07570.1358-0.03990.1050.09420.02290.00560.15460.00330.1541-29.5635-19.1398-30.2085
20.78030.176-0.19930.72061.00251.72320.00810.04730.06080.05220.2114-0.09070.08560.2247-0.21950.01480.0394-0.04490.2656-0.08720.15312.3285-5.8028-38.1662
31.1563-0.618-0.19631.93570.88990.45430.0591-0.00160.0110.0444-0.08410.14010.00550.01920.0250.06170.00380.00580.1735-0.06420.1331-38.061330.6851-7.8043
41.2582-0.2280.7830.1511-0.00270.72880.0609-0.1530.08330.0217-0.0453-0.09170.0303-0.1923-0.01560.0549-0.0224-0.0450.2929-0.10230.1565-5.862424.60967.1002
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 349
2X-RAY DIFFRACTION2B17 - 349
3X-RAY DIFFRACTION3C17 - 349
4X-RAY DIFFRACTION4D17 - 349

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