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- PDB-5dce: Neisseria meningitidis 3-deoxy-D-arabino-heptulosonate 7-phosphat... -

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Basic information

Entry
Database: PDB / ID: 5dce
TitleNeisseria meningitidis 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase regulated (Tryptophan)
ComponentsPhospho-2-dehydro-3-deoxyheptonate aldolase
KeywordsTRANSFERASE / Allostery / aromatic amino acids / 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 / 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
: / TRYPTOPHAN / Phospho-2-dehydro-3-deoxyheptonate aldolase
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.23 Å
AuthorsHeyes, L.C. / Parker, E.J.
CitationJournal: Plos One / Year: 2016
Title: The Functional Unit of Neisseria meningitidis 3-Deoxy--Arabino-Heptulosonate 7-Phosphate Synthase Is Dimeric.
Authors: Cross, P.J. / Heyes, L.C. / Zhang, S. / Nazmi, A.R. / Parker, E.J.
History
DepositionAug 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
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 / diffrn_source / 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)155,88512
Polymers154,8494
Non-polymers1,0378
Water3,891216
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.432, 138.042, 75.868
Angle α, β, γ (deg.)90.00, 96.58, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12C
22A
13D
23A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115B6 - 351
2115A6 - 351
1125C6 - 351
2125A6 - 351
1135D6 - 351
2135A6 - 351

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.954944, -0.235275, -0.180906), (-0.227877, 0.190742, 0.954824), (-0.19014, 0.953028, -0.235762)-34.40364, 20.54096, -34.03052
3given(1), (1), (1)
4given(0.954339, 0.227203, 0.193948), (0.225674, -0.973733, 0.030243), (0.195725, 0.014907, -0.980546)0.11231, 23.6158, -30.94841
5given(1), (1), (1)
6given(-0.999978, 0.006532, -0.001182), (-0.000183, -0.205138, -0.978733), (-0.006636, -0.978711, 0.205134)-34.56956, -5.27841, -4.24637

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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 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-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H12N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.51 Å3/Da / Density % sol: 51.09 % / 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: Jul 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.23→75.37 Å / Num. obs: 72956 / % possible obs: 99.9 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 14.6
Reflection shellResolution: 2.23→2.28 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.23→75.37 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 17.469 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.277 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23784 4531 6.2 %RANDOM
Rwork0.19153 ---
obs0.19449 68391 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.745 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å20 Å2-0.02 Å2
2--2.69 Å20 Å2
3----1.17 Å2
Refinement stepCycle: 1 / Resolution: 2.23→75.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10260 0 64 216 10540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01910539
X-RAY DIFFRACTIONr_bond_other_d0.0020.029892
X-RAY DIFFRACTIONr_angle_refined_deg1.2621.95614326
X-RAY DIFFRACTIONr_angle_other_deg0.775322664
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.34951379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.87824.108443
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.503151664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4431562
X-RAY DIFFRACTIONr_chiral_restr0.0720.21638
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02112163
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022355
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_it1.7563.3465531
X-RAY DIFFRACTIONr_mcbond_other1.7553.3455530
X-RAY DIFFRACTIONr_mcangle_it2.8155.0096902
X-RAY DIFFRACTIONr_mcangle_other2.8155.016903
X-RAY DIFFRACTIONr_scbond_it1.853.485008
X-RAY DIFFRACTIONr_scbond_other1.853.485008
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9645.1687424
X-RAY DIFFRACTIONr_long_range_B_refined5.18126.87211949
X-RAY DIFFRACTIONr_long_range_B_other5.18126.87511950
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B2003MEDIUM POSITIONAL0.090.5
1B2828LOOSE POSITIONAL0.295
1B2003MEDIUM THERMAL2.82
1B2828LOOSE THERMAL2.8510
2C2013MEDIUM POSITIONAL0.090.5
2C2896LOOSE POSITIONAL0.255
2C2013MEDIUM THERMAL2.662
2C2896LOOSE THERMAL3.0310
3D2015MEDIUM POSITIONAL0.080.5
3D2976LOOSE POSITIONAL0.235
3D2015MEDIUM THERMAL2.652
3D2976LOOSE THERMAL2.7410
LS refinement shellResolution: 2.23→2.288 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 466 -
Rwork0.319 4883 -
obs--99.85 %
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)
12.1831-0.06180.17871.61750.67930.9930.1048-0.0586-0.20520.2266-0.16080.12860.1594-0.10810.0560.044-0.02620.02430.043-0.00210.1376-28.4719-16.1584-29.6176
22.93430.225-0.39221.51641.50993.20350.02010.35040.05130.08820.3439-0.28060.21670.5783-0.3640.01970.0621-0.01670.2521-0.08680.20291.9594-3.9619-37.0443
33.1098-0.450.55892.40510.28071.0488-0.1262-0.46840.33370.14180.13450.1937-0.1305-0.179-0.00830.0620.03710.06890.1882-0.10550.2186-36.373232.0928-7.9961
41.86870.12310.6810.91020.05131.19670.0244-0.48340.16260.1370.0677-0.24340.0592-0.1312-0.09210.02540.0079-0.03050.3382-0.22310.2733-6.413826.95685.3542
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 349
2X-RAY DIFFRACTION2B8 - 349
3X-RAY DIFFRACTION3C6 - 350
4X-RAY DIFFRACTION4D3 - 350

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