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- PDB-5ugj: Crystal structure of HTPA Reductase from neisseria meningitidis -

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Basic information

Entry
Database: PDB / ID: 5ugj
TitleCrystal structure of HTPA Reductase from neisseria meningitidis
Components4-hydroxy-tetrahydrodipicolinate reductase
KeywordsOXIDOREDUCTASE / HTPA Reductase Lysine biosynthesis DHDPR
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate reductase / oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor / 4-hydroxy-tetrahydrodipicolinate reductase / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / NAD binding / NADP binding / cytosol
Similarity search - Function
Dihydrodipicolinate reductase, conserved site / Dihydrodipicolinate reductase signature. / Dihydrodipicolinate reductase, C-terminal / Dihydrodipicolinate reductase / Dihydrodipicolinate reductase, C-terminus / Dihydrodipicolinate reductase, N-terminal / Dihydrodipicolinate reductase, N-terminus / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain ...Dihydrodipicolinate reductase, conserved site / Dihydrodipicolinate reductase signature. / Dihydrodipicolinate reductase, C-terminal / Dihydrodipicolinate reductase / Dihydrodipicolinate reductase, C-terminus / Dihydrodipicolinate reductase, N-terminal / Dihydrodipicolinate reductase, N-terminus / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4-hydroxy-tetrahydrodipicolinate reductase
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKeown, J.K. / Richards, E.W. / Pearce, F.G. / Goldstone, D.C.
CitationJournal: Biochem. J. / Year: 2018
Title: Plant DHDPR forms a dimer with unique secondary structure features that preclude higher-order assembly.
Authors: Watkin, S.A.J. / Keown, J.R. / Richards, E. / Goldstone, D.C. / Devenish, S.R.A. / Grant Pearce, F.
History
DepositionJan 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-hydroxy-tetrahydrodipicolinate reductase
B: 4-hydroxy-tetrahydrodipicolinate reductase
C: 4-hydroxy-tetrahydrodipicolinate reductase
D: 4-hydroxy-tetrahydrodipicolinate reductase


Theoretical massNumber of molelcules
Total (without water)128,5534
Polymers128,5534
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11860 Å2
ΔGint-29 kcal/mol
Surface area42150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.866, 66.748, 133.535
Angle α, β, γ (deg.)90.000, 105.120, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUGLYGLYAA4 - 26537 - 298
21LEULEUGLYGLYBB4 - 26537 - 298
12LEULEUGLYGLYAA4 - 26537 - 298
22LEULEUGLYGLYCC4 - 26537 - 298
13LEULEUGLYGLYAA4 - 26537 - 298
23LEULEUGLYGLYDD4 - 26537 - 298
14PROPROLEULEUBB3 - 26636 - 299
24PROPROLEULEUCC3 - 26636 - 299
15PROPROLEULEUBB3 - 26636 - 299
25PROPROLEULEUDD3 - 26636 - 299
16THRTHRASNASNCC2 - 26735 - 300
26THRTHRASNASNDD2 - 26735 - 300

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
4-hydroxy-tetrahydrodipicolinate reductase / / HTPA reductase


Mass: 32138.309 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: dapB, NMB0203 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9K1F1, 4-hydroxy-tetrahydrodipicolinate reductase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.03 mM CaCl2, 0.03 mM MgCl2, 20% v/v PEG 500 MME, 10% w/v PEG 20000, and 0.1 M Trizma/BICINE pH 8.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.7→47.44 Å / Num. obs: 30159 / % possible obs: 92 % / Redundancy: 2.9 % / CC1/2: 0.992 / Rmerge(I) obs: 0.088 / Net I/σ(I): 7.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.7-2.832.80.4110.669193.8
8.96-47.442.90.0280.996199.6

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Processing

Software
NameVersionClassification
Aimless0.5.8data scaling
REFMACrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ARZ

1arz


Resolution: 2.7→47.44 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.904 / SU B: 15.881 / SU ML: 0.307 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.37 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2501 1592 5.3 %RANDOM
Rwork0.2065 ---
obs0.2088 28567 91.47 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 237.57 Å2 / Biso mean: 62.326 Å2 / Biso min: 15.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20 Å20.81 Å2
2---1.87 Å20 Å2
3---2.02 Å2
Refinement stepCycle: final / Resolution: 2.7→47.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7776 0 0 36 7812
Biso mean---33.97 -
Num. residues----1060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0197899
X-RAY DIFFRACTIONr_angle_refined_deg1.7241.94310723
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.28551056
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37424.154325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.587151239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5541547
X-RAY DIFFRACTIONr_chiral_restr0.1220.21274
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025931
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A139240.16
12B139240.16
21A140800.16
22C140800.16
31A138320.17
32D138320.17
41B148260.12
42C148260.12
51B140560.15
52D140560.15
61C143400.16
62D143400.16
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 119 -
Rwork0.313 2168 -
all-2287 -
obs--93.58 %

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