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- PDB-6bdx: 4-hydroxy tetrahydrodipicolinate reductase from Neisseria gonorrhoeae -

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Basic information

Entry
Database: PDB / ID: 6bdx
Title4-hydroxy tetrahydrodipicolinate reductase from Neisseria gonorrhoeae
Components4-hydroxy-tetrahydrodipicolinate reductase
KeywordsOXIDOREDUCTASE / Lysine biosynthesis / 4-hydroxy tetrahydrodipicolinate reductase / Neisseria gonorrhoeae
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 / cytoplasm
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 / 4-hydroxy-tetrahydrodipicolinate reductase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPote, S.S. / Pye, S.E. / Sheahan, T.E. / Chruszcz, M.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: 4-Hydroxy-tetrahydrodipicolinate reductase from Neisseria gonorrhoeae - structure and interactions with coenzymes and substrate analog.
Authors: Pote, S. / Pye, S.E. / Sheahan, T.E. / Gawlicka-Chruszcz, A. / Majorek, K.A. / Chruszcz, M.
History
DepositionOct 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1319
Polymers28,3621
Non-polymers7698
Water3,117173
1
A: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules

A: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules

A: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules

A: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,52336
Polymers113,4494
Non-polymers3,07432
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area15520 Å2
ΔGint-406 kcal/mol
Surface area41320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.803, 71.723, 138.414
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 28362.170 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria)
Gene: dapB, WHOK_00270, WHOK_02229C, WHOM_00688, WHOM_02238C, WHOP_00630, WHOP_02238C, WHOU_00751, WHOU_02311C, WHOV_01184, WHOV_02299C, WHOW_00218, WHOW_02292C, WHOX_00871, WHOX_02228C, WHOY_00570, ...Gene: dapB, WHOK_00270, WHOK_02229C, WHOM_00688, WHOM_02238C, WHOP_00630, WHOP_02238C, WHOU_00751, WHOU_02311C, WHOV_01184, WHOV_02299C, WHOW_00218, WHOW_02292C, WHOX_00871, WHOX_02228C, WHOY_00570, WHOY_02311C, WHOZ_01787, WHOZ_02300C
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A1D3EVW8, UniProt: Q5F5Y7*PLUS, 4-hydroxy-tetrahydrodipicolinate reductase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.53 Å3/Da / Density % sol: 51.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M BIS-TRIS pH 6.5, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. obs: 25492 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 7.9 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.024 / Rrim(I) all: 0.067 / Rsym value: 0.061 / Net I/σ(I): 48.2
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.784 / Mean I/σ(I) obs: 3.38 / Num. unique obs: 1251 / Rpim(I) all: 0.27 / Rrim(I) all: 0.757 / Rsym value: 0.784 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
MOLREPphasing
HKL-3000refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ARZ

1arz


Resolution: 1.85→40 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.117 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20989 1173 4.7 %RANDOM
Rwork0.16943 ---
obs0.17139 23783 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.09 Å2
Baniso -1Baniso -2Baniso -3
1-2.3 Å20 Å2-0 Å2
2---0.67 Å20 Å2
3----1.63 Å2
Refinement stepCycle: 1 / Resolution: 1.85→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1885 0 40 173 2098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191944
X-RAY DIFFRACTIONr_bond_other_d00.021821
X-RAY DIFFRACTIONr_angle_refined_deg1.9111.9682639
X-RAY DIFFRACTIONr_angle_other_deg3.83334185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9365258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50523.73375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.18115299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9081513
X-RAY DIFFRACTIONr_chiral_restr0.1330.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022178
X-RAY DIFFRACTIONr_gen_planes_other0.010.02379
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_it2.3382.9871038
X-RAY DIFFRACTIONr_mcbond_other2.3382.9841037
X-RAY DIFFRACTIONr_mcangle_it3.2594.451294
X-RAY DIFFRACTIONr_mcangle_other3.2584.4531295
X-RAY DIFFRACTIONr_scbond_it3.8443.632906
X-RAY DIFFRACTIONr_scbond_other3.3213.447875
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2034.9741297
X-RAY DIFFRACTIONr_long_range_B_refined7.10937.0122024
X-RAY DIFFRACTIONr_long_range_B_other6.96836.481999
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 82 -
Rwork0.216 1715 -
obs--100 %
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)
11.09670.04560.16170.73320.55970.6611-0.0194-0.03180.01480.05750.00540.00620.01780.04260.01410.0081-0.00610.00430.04440.01130.0793-23.40617.40631.691
20.1854-0.01970.07120.3597-0.01810.80260.01690.0543-0.01090.04040.0047-0.02850.04740.1431-0.02170.00940.0159-0.00940.0958-0.01170.0384-19.01624.3490.96
30.9462-0.45880.38972.129-0.41611.25030.02650.1242-0.1034-0.1896-0.05080.1364-0.0519-0.02110.02430.02550.0014-0.02050.0473-0.0040.081-27.41513.15618.89
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 123
2X-RAY DIFFRACTION2A124 - 236
3X-RAY DIFFRACTION3A237 - 267

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