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- PDB-5tek: Apo Structure of 4-Hydroxy-tetrahydrodipicolinate Reductase from ... -

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Basic information

Entry
Database: PDB / ID: 5tek
TitleApo Structure of 4-Hydroxy-tetrahydrodipicolinate Reductase from Mycobacterium tuberculosis
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 / 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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
4-hydroxy-tetrahydrodipicolinate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsMank, N. / Pote, S. / 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 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
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 / _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
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,9009
Polymers52,3592
Non-polymers5417
Water2,900161
1
A: 4-hydroxy-tetrahydrodipicolinate reductase
B: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)105,80118
Polymers104,7194
Non-polymers1,08214
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area15040 Å2
ΔGint-132 kcal/mol
Surface area39360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.569, 122.607, 80.846
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
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 0 / Auth seq-ID: 0 - 244 / Label seq-ID: 4 - 248

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 26179.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra) (bacteria)
Strain: ATCC 25177 / H37Ra / Gene: dapB, MRA_2798 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A5U6C6, 4-hydroxy-tetrahydrodipicolinate reductase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium Chloride, 0.1 M HEPES pH 7.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 40777 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/av σ(I): 42.383 / Net I/σ(I): 13
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2-2.034.80.6550.856199.3
2.03-2.075.30.5830.9071100
2.07-2.115.70.4770.9341100
2.11-2.155.70.4360.9291100
2.15-2.25.70.3550.961100
2.2-2.255.60.3330.9481100
2.25-2.315.70.2580.9731100
2.31-2.375.70.2010.9851100
2.37-2.445.70.1650.9841100
2.44-2.525.70.1390.9891100
2.52-2.615.70.1190.9921100
2.61-2.715.70.1020.9931100
2.71-2.845.70.0910.9941100
2.84-2.995.60.0760.9961100
2.99-3.175.60.0660.997199.9
3.17-3.425.50.060.997199.7
3.42-3.765.40.0520.998199.8
3.76-4.315.30.0480.998199
4.31-5.425.40.0440.998198.8
5.42-404.90.0490.994196.5

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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: 1YL5

1yl5


Resolution: 2.01→40 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.139
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2167 2023 5 %RANDOM
Rwork0.192 ---
obs0.1932 38724 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 112.29 Å2 / Biso mean: 55.381 Å2 / Biso min: 31.13 Å2
Baniso -1Baniso -2Baniso -3
1-3.68 Å20 Å20 Å2
2---1.4 Å20 Å2
3----2.27 Å2
Refinement stepCycle: final / Resolution: 2.01→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3639 0 22 161 3822
Biso mean--71.18 60.45 -
Num. residues----496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193723
X-RAY DIFFRACTIONr_bond_other_d00.023635
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.9685070
X-RAY DIFFRACTIONr_angle_other_deg3.74538337
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5615494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.27923.681144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89815564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1141525
X-RAY DIFFRACTIONr_chiral_restr0.080.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214235
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02796
X-RAY DIFFRACTIONr_mcbond_it1.8113.4941982
X-RAY DIFFRACTIONr_mcbond_other1.813.4921981
X-RAY DIFFRACTIONr_mcangle_it2.8025.2282474
Refine LS restraints NCS

Ens-ID: 1 / Number: 27680 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.005→2.057 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 110 -
Rwork0.349 2604 -
all-2714 -
obs--90.86 %
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)
15.1113-0.6647-1.91658.04490.14540.73030.4494-0.65990.22960.0436-0.3677-0.9116-0.2280.2602-0.08160.5204-0.1701-0.03020.4101-0.02260.1717-3.64131.66511.25
23.5197-0.63370.30272.82011.32256.28420.0414-0.1311-0.0288-0.1461-0.24220.3280.325-0.38290.20090.08360.019-0.02060.1394-0.03260.0428-18.97719.825.985
31.6303-0.8228-0.5024.3939-0.21951.4992-0.0791-0.045-0.25480.30830.13550.7353-0.2804-0.4506-0.05640.10740.08320.05550.20090.05660.1423-14.2583.956-21.128
43.6555-2.8511-2.56493.14473.52745.47560.17370.00470.1377-0.3848-0.0837-0.1004-0.11370.2128-0.090.26120.087-0.0070.24540.01930.0089-10.44419.837-4.622
52.5695-0.2541.68763.9496-1.12436.0037-0.08890.3708-0.125-0.2590.0612-0.05450.44950.25860.02780.1311-0.00140.00210.2155-0.03210.0133-5.44521.638-54.187
61.83541.08090.06472.48370.28873.1513-0.20090.15160.12080.06410.1232-0.1134-0.24070.47310.07770.0921-0.0096-0.03920.1984-0.00310.06780.77630.833-43.486
73.1221-1.5466-1.48272.6265-0.48073.4940.05850.15530.49980.1424-0.1586-0.5941-0.55440.12640.10.2227-0.0539-0.0290.0872-0.01430.23055.64815.908-23.972
82.0799-1.741-0.43834.21280.26142.4639-0.0363-0.13870.52540.2536-0.0057-0.9844-0.2440.40170.0420.1237-0.0768-0.0570.1481-0.05670.313211.75410.337-19.606
90.663-0.6390.69083.5052-3.2553.0471-0.0563-0.04660.09850.20420.12430.084-0.1624-0.1045-0.0680.24340.07960.0130.1894-0.02320.074-6.08518.713-33.201
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 3
2X-RAY DIFFRACTION2A4 - 107
3X-RAY DIFFRACTION3A108 - 211
4X-RAY DIFFRACTION4A212 - 245
5X-RAY DIFFRACTION5B0 - 51
6X-RAY DIFFRACTION6B52 - 112
7X-RAY DIFFRACTION7B113 - 157
8X-RAY DIFFRACTION8B158 - 201
9X-RAY DIFFRACTION9B202 - 246

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