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

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Basic information

Entry
Database: PDB / ID: 5czs
TitleNeisseria meningitidis 3 dexy-D-arabino-heptulosonate 7-phosphate synthase Glu98Ala variant regulated
ComponentsPhospho-2-dehydro-3-deoxyheptonate aldolase
KeywordsTRANSFERASE / Regulated DAH7PS
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
: / DI(HYDROXYETHYL)ETHER / PHOSPHOENOLPYRUVATE / PHENYLALANINE / Phospho-2-dehydro-3-deoxyheptonate aldolase
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsHeyes, L.C. / Parker, E.J.
CitationJournal: To Be Published
Title: Structure of Neisseria meningitidis 3 dexy-D-arabino-heptulosonate 7-phosphate synthase Glu98Ala variant at 2.42 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 1.2Sep 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 / pdbx_initial_refinement_model / 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)156,46120
Polymers154,6164
Non-polymers1,84516
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17220 Å2
ΔGint-101 kcal/mol
Surface area45120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.322, 142.326, 74.591
Angle α, β, γ (deg.)90.00, 96.84, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTetramer by Analytical gel filtration

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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 , 6 types, 347 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-PEP / PHOSPHOENOLPYRUVATE


Mass: 168.042 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5O6P
#4: Chemical
ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H11NO2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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
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: Oct 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.42→74.06 Å / Num. obs: 57783 / % possible obs: 99.8 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.156 / Net I/σ(I): 11
Reflection shellResolution: 2.42→2.47 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.906 / Mean I/σ(I) obs: 2 / % possible all: 97.1

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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: 2.42→74.06 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.901 / SU B: 18.179 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.477 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24569 3507 6.1 %RANDOM
Rwork0.19104 ---
obs0.19458 54228 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.26 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å20 Å20.45 Å2
2--2.65 Å20 Å2
3----1.01 Å2
Refinement stepCycle: 1 / Resolution: 2.42→74.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10439 0 111 331 10881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01910749
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210202
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.96314566
X-RAY DIFFRACTIONr_angle_other_deg0.797323403
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.56951372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.60224.038468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16151760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5611567
X-RAY DIFFRACTIONr_chiral_restr0.0720.21639
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02112273
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022404
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_it1.1852.3045521
X-RAY DIFFRACTIONr_mcbond_other1.1842.3045520
X-RAY DIFFRACTIONr_mcangle_it1.9653.4446882
X-RAY DIFFRACTIONr_mcangle_other1.9653.4446883
X-RAY DIFFRACTIONr_scbond_it1.2682.4355228
X-RAY DIFFRACTIONr_scbond_other1.2682.4355228
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0873.6047685
X-RAY DIFFRACTIONr_long_range_B_refined3.99818.55612288
X-RAY DIFFRACTIONr_long_range_B_other3.99818.55812289
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.42→2.483 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 222 -
Rwork0.266 3951 -
obs--97.55 %
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)
10.77960.09330.09471.00750.12630.56740.08140.0082-0.03250.1348-0.03330.08810.1338-0.0546-0.04820.13210.0019-0.02130.0091-0.00120.1227-28.2499-13.4615-28.7294
21.04170.1906-0.57860.85740.06471.2103-0.0450.0254-0.1368-0.04880.022-0.19010.12160.180.02310.04720.0369-0.00960.0523-0.03120.15591.6142-2.2527-36.6595
30.7036-0.21950.16531.20690.27440.65610.0028-0.0479-0.00570.1017-0.01430.1439-0.0346-0.04680.01150.0984-0.01360.02480.0084-0.0110.1344-36.775335.5833-8.7007
41.0188-0.00130.41150.475-0.13950.85420.0567-0.06770.0190.1194-0.0605-0.0668-0.0231-0.01580.00370.1216-0.0304-0.01660.0186-0.0130.0965-6.795931.11114.6925
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 DIFFRACTION4D3 - 349

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