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

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Basic information

Entry
Database: PDB / ID: 5czt
TitleNeisseria meningitidis 3 dexy-D-arabino-heptulosonate 7-phosphate synthase Glu176Ala variant
ComponentsPhospho-2-dehydro-3-deoxyheptonate aldolase
KeywordsTRANSFERASE / DAH7PS / Allostery
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
: / PHENYLALANINE / Phospho-2-dehydro-3-deoxyheptonate aldolase
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.04 Å
AuthorsHeyes, L.C. / Parker, E.J.
CitationJournal: To Be Published
Title: Neisseria meningitidis 3 dexy-D-arabino-heptulosonate 7-phosphate synthase Glu176Ala variant at 2.04 Angstroms resolution
Authors: Heyes, L.C. / Parker, E.J.
History
DepositionAug 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Derived calculations / Structure summary
Category: diffrn_source / pdbx_struct_assembly_auth_evidence ...diffrn_source / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list / struct_keywords
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.pdbx_keywords
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)155,60315
Polymers154,6164
Non-polymers98711
Water13,421745
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15320 Å2
ΔGint-134 kcal/mol
Surface area45330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.647, 140.828, 77.266
Angle α, β, γ (deg.)90.00, 98.56, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTetramer by Analytical gel filtration

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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: 38654.102 Da / Num. of mol.: 4
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
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-PHE / PHENYLALANINE / Phenylalanine


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H11NO2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 745 / 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: 2.68 Å3/Da / Density % sol: 54.09 % / 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
PH range: 7.3

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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: Jun 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.04→76.41 Å / Num. obs: 101442 / % possible obs: 99.9 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 18.6
Reflection shellResolution: 2.04→2.08 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 2.6 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.04→76.41 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 8.059 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20566 6322 6.2 %RANDOM
Rwork0.17057 ---
obs0.17282 95084 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.738 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å2-0.63 Å2
2--1.23 Å20 Å2
3----1.16 Å2
Refinement stepCycle: LAST / Resolution: 2.04→76.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10503 0 55 745 11303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01910803
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210353
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.95914633
X-RAY DIFFRACTIONr_angle_other_deg0.807323773
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.55751385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.98523.683467
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.592151818
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.861575
X-RAY DIFFRACTIONr_chiral_restr0.080.21646
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112332
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022437
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_it1.2842.1325555
X-RAY DIFFRACTIONr_mcbond_other1.2842.1325554
X-RAY DIFFRACTIONr_mcangle_it2.033.1886935
X-RAY DIFFRACTIONr_mcangle_other2.0293.1886936
X-RAY DIFFRACTIONr_scbond_it1.6642.3185248
X-RAY DIFFRACTIONr_scbond_other1.6642.3185248
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6143.4017699
X-RAY DIFFRACTIONr_long_range_B_refined5.02917.81912741
X-RAY DIFFRACTIONr_long_range_B_other5.02917.81912742
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.04→2.093 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 483 -
Rwork0.246 6897 -
obs--98.94 %
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)
10.215-0.19790.04110.87580.03361.21810.02260.0894-0.0063-0.0269-0.14-0.157-0.04650.1820.11730.00850.01470.00340.10460.06620.1156-3.5771-11.9248-40.0227
21.0563-0.42770.9020.3946-0.0441.6683-0.03750.0679-0.07970.10710.06450.0253-0.05820.2036-0.0270.10180.0055-0.03770.07480.03930.07416.1235-9.6737-7.9745
30.3501-0.0230.02740.5877-0.09720.6554-0.0090.01180.03490.0015-0.0221-0.00110.0121-0.01080.03120.055-0.0222-0.01480.0368-0.00150.03-23.420936.6974-32.1863
40.4356-0.0085-0.0670.30130.01710.66460.0067-0.0660.01420.07830.03340.05350.082-0.1055-0.04020.0853-0.01110.01980.06770.02220.0191-33.691525.7628-1.9161
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 349
2X-RAY DIFFRACTION2B4 - 349
3X-RAY DIFFRACTION3C4 - 349
4X-RAY DIFFRACTION4D4 - 349

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