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- PDB-5tem: Structure of 4-Hydroxy-tetrahydrodipicolinate Reductase from Vibr... -

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Basic information

Entry
Database: PDB / ID: 5tem
TitleStructure of 4-Hydroxy-tetrahydrodipicolinate Reductase from Vibrio vulnificus with 2,6 Pyridine Dicarboxylic and NADH
Components4-hydroxy-tetrahydrodipicolinate reductase
KeywordsOXIDOREDUCTASE / Lysine Biosynthesis
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PYRIDINE-2,6-DICARBOXYLIC ACID / 4-hydroxy-tetrahydrodipicolinate reductase
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMank, N. / Arnette, K. / Klapper, V. / Chruszcz, M.
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2021
Title: Comparative structural and mechanistic studies of 4-hydroxy-tetrahydrodipicolinate reductases from Mycobacterium tuberculosis and Vibrio vulnificus.
Authors: Pote, S. / Kachhap, S. / Mank, N.J. / Daneshian, L. / Klapper, V. / Pye, S. / Arnette, A.K. / Shimizu, L.S. / Borowski, T. / Chruszcz, M.
History
DepositionSep 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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
C: 4-hydroxy-tetrahydrodipicolinate reductase
A: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,38910
Polymers57,3432
Non-polymers2,0458
Water4,414245
1
C: 4-hydroxy-tetrahydrodipicolinate reductase
A: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules

C: 4-hydroxy-tetrahydrodipicolinate reductase
A: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,77720
Polymers114,6874
Non-polymers4,09116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area19240 Å2
ΔGint-125 kcal/mol
Surface area38430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.639, 112.588, 62.432
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21A

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 1 - 266 / Label seq-ID: 1 - 266

Dom-IDAuth asym-IDLabel asym-ID
1CA
2AB

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Components

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


Mass: 28671.691 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: CMCP6 / Gene: dapB, VV1_0567 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8DEM0, 4-hydroxy-tetrahydrodipicolinate reductase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-PDC / PYRIDINE-2,6-DICARBOXYLIC ACID / DIPICOLINIC ACID


Mass: 167.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5NO4
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.5 Å3/Da / Density % sol: 50.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→65.56 Å / Num. obs: 28190 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/av σ(I): 12.762 / Net I/σ(I): 6.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.2-2.244.60.4932.10.851195.7
2.24-2.284.60.4850.865197.3
2.28-2.324.70.4230.899197.3
2.32-2.374.70.4160.887196.5
2.37-2.424.70.3310.927197.5
2.42-2.484.70.2960.944196.9
2.48-2.544.70.2730.949196.8
2.54-2.614.70.2540.953196.3
2.61-2.694.70.2050.98196.2
2.69-2.774.70.2040.969196.4
2.77-2.874.70.1760.978195.9
2.87-2.994.70.1440.986195.7
2.99-3.124.80.1260.988195.7
3.12-3.294.80.1050.991195.1
3.29-3.494.70.0860.994194.9
3.49-3.764.70.0750.995194.6
3.76-4.144.70.0690.996194.1
4.14-4.744.60.0620.996193.5
4.74-5.974.70.0580.997192.5
5.97-504.40.0550.998189.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ARZ

1arz


Resolution: 2.2→65.56 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.941 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.291 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2236 1368 4.9 %RANDOM
Rwork0.1908 ---
obs0.1925 26798 95.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 103.39 Å2 / Biso mean: 32.26 Å2 / Biso min: 9.19 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å2-0 Å2
2---1.83 Å20 Å2
3---0.53 Å2
Refinement stepCycle: final / Resolution: 2.2→65.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3929 0 132 245 4306
Biso mean--36.91 33.49 -
Num. residues----532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194125
X-RAY DIFFRACTIONr_bond_other_d00.023899
X-RAY DIFFRACTIONr_angle_refined_deg1.7161.9835606
X-RAY DIFFRACTIONr_angle_other_deg3.83138932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8795530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91924.611167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35715647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3881522
X-RAY DIFFRACTIONr_chiral_restr0.0930.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024694
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02908
X-RAY DIFFRACTIONr_mcbond_it1.4772.0752126
X-RAY DIFFRACTIONr_mcbond_other1.4762.0742125
X-RAY DIFFRACTIONr_mcangle_it2.4483.1042654
Refine LS restraints NCS

Ens-ID: 1 / Number: 30406 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1C
2A
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 110 -
Rwork0.272 1918 -
all-2028 -
obs--94.11 %
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)
12.41361.5636-1.14471.3916-1.54133.13960.0336-0.2106-0.1396-0.08510.01-0.15240.1893-0.0899-0.04360.2501-0.04150.01550.0931-0.03570.1072-54.082-30.675-22.676
24.7946-5.7252-3.86759.14393.67753.5107-0.00360.2608-0.62920.2815-0.891-0.2493-0.1410.05270.89450.1736-0.1857-0.03120.26860.13350.5809-44.963-36.003-31.847
312.83712.70693.46171.6676-1.96697.5706-0.03880.5569-0.1737-0.03750.0539-0.05610.07830.2944-0.01520.1133-0.04180.00380.06690.02280.097-47.899-37.463-20.289
40.38040.47530.16941.5798-1.26232.2858-0.1240.0636-0.0981-0.22850.1713-0.12340.0543-0.1007-0.04730.2534-0.05420.01690.035-0.02070.0297-58.732-26.569-35.59
50.29910.47810.07340.78940.07480.1931-0.03950.02-0.0076-0.04030.027-0.0176-0.0328-0.07130.01240.23240.0022-0.00270.0742-0.00120.0092-54.053-6.186-26.526
63.0451-0.6439-1.23482.04392.04212.18140.02150.1533-0.00870.00140.0411-0.04080.0379-0.0005-0.06260.23830.0362-0.00060.03290.03080.0652-29.251-31.712-8.619
71.1111.37151.0152.00110.6127.73760.0252-0.0314-0.1007-0.0415-0.00120.06560.2874-0.4089-0.0240.0529-0.003-0.02360.07140.00350.1748-37.821-37.064-4.506
80.6501-0.04520.09610.9599-0.18011.6881-0.0442-0.01680.00130.12330.13120.0455-0.01290.0731-0.08690.20990.0459-0.00410.05010.00690.0085-23.447-26.1363.634
90.3627-0.10970.04471.0059-0.14410.05090.0037-0.0692-0.03240.0149-0.022-0.01270.01330.02470.01820.25340.0075-0.01450.05760.01880.0226-30.74-1.747-4.701
101.3330.69422.30734.1851.49374.0201-0.16780.2477-0.0963-0.36630.3337-0.076-0.30630.453-0.16590.1463-0.00290.0430.1369-0.0160.0173-17.205-21.984-7.769
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 34
2X-RAY DIFFRACTION2A35 - 46
3X-RAY DIFFRACTION3A47 - 56
4X-RAY DIFFRACTION4A57 - 111
5X-RAY DIFFRACTION5A112 - 266
6X-RAY DIFFRACTION6C1 - 34
7X-RAY DIFFRACTION7C35 - 56
8X-RAY DIFFRACTION8C57 - 127
9X-RAY DIFFRACTION9C128 - 239
10X-RAY DIFFRACTION10C240 - 266

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