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

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Basic information

Entry
Database: PDB / ID: 5tej
TitleStructure of 4-Hydroxy-tetrahydrodipicolinate Reductase from Vibrio vulnificus with 2,5 Furan 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
2,5 Furan Dicarboxylic Acid / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / TRIETHYLENE GLYCOL / 4-hydroxy-tetrahydrodipicolinate reductase
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 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 ...citation / citation_author / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,47317
Polymers114,9154
Non-polymers3,55813
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17690 Å2
ΔGint-78 kcal/mol
Surface area39220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.059, 91.039, 125.922
Angle α, β, γ (deg.)90.000, 120.070, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 2692 - 270
21BB1 - 2692 - 270
12AA1 - 2662 - 267
22CC1 - 2662 - 267
13AA1 - 2692 - 270
23DD1 - 2692 - 270
14BB1 - 2662 - 267
24CC1 - 2662 - 267
15BB1 - 2692 - 270
25DD1 - 2692 - 270
16CC1 - 2662 - 267
26DD1 - 2662 - 267

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 28728.744 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (strain CMCP6) (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

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Non-polymers , 6 types, 270 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-7FN / 2,5 Furan Dicarboxylic Acid


Mass: 156.093 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H4O5
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 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: Jun 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→50.01 Å / Num. obs: 43079 / % possible obs: 100 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.113 / Rsym value: 0.113 / Net I/av σ(I): 16.725 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.49-2.533.50.4642.80.8199.5
2.53-2.5840.4670.8341100
2.58-2.634.20.4490.8621100
2.63-2.684.30.3840.8971100
2.68-2.744.30.3310.9251100
2.74-2.84.30.3080.9311100
2.8-2.874.30.2670.9441100
2.87-2.954.30.2210.9591100
2.95-3.044.30.1960.9691100
3.04-3.144.30.1610.9811100
3.14-3.254.30.1430.9841100
3.25-3.384.30.1130.9911100
3.38-3.534.30.1040.991100
3.53-3.724.30.0850.9941100
3.72-3.954.30.0810.9941100
3.95-4.264.30.0760.9941100
4.26-4.694.20.0720.9951100
4.69-5.364.20.0780.9931100
5.36-6.754.20.0830.9931100
6.75-5040.0610.996199.7

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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: 2.5→50.01 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.502 / ESU R Free: 0.245
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2117 2095 4.9 %RANDOM
Rwork0.1816 ---
obs0.1831 40949 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 108.03 Å2 / Biso mean: 36.786 Å2 / Biso min: 14.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20 Å2-0.1 Å2
2--0.8 Å2-0 Å2
3----0.97 Å2
Refinement stepCycle: final / Resolution: 2.5→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7952 0 236 257 8445
Biso mean--37.79 32.49 -
Num. residues----1075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0198318
X-RAY DIFFRACTIONr_bond_other_d00.027923
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.97911289
X-RAY DIFFRACTIONr_angle_other_deg3.719318163
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.06351071
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1624.69339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.231151319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8591544
X-RAY DIFFRACTIONr_chiral_restr0.0840.21309
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029478
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021825
X-RAY DIFFRACTIONr_mcbond_it1.0472.2974296
X-RAY DIFFRACTIONr_mcbond_other1.0472.2964295
X-RAY DIFFRACTIONr_mcangle_it1.8513.4385363
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A294560.14
12B294560.14
21A292600.13
22C292600.13
31A297660.13
32D297660.13
41B301060.12
42C301060.12
51B308460.11
52D308460.11
61C302440.11
62D302440.11
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 165 -
Rwork0.251 2896 -
all-3061 -
obs--97.27 %
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)
13.37291.85481.76156.0168-0.56967.385-0.20260.07490.3071-0.1030.16430.6478-0.3777-0.06760.03840.0398-0.0475-0.01520.1440.00750.0748-3.436-16.68747.773
24.5191-2.90690.66977.1829-1.15738.9336-0.3670.15720.35990.29730.37350.92-0.861-0.3699-0.00650.1861-0.0622-0.01570.24380.08540.2833-8.845-11.10455.379
31.2670.332-0.86210.1255-0.44041.95470.0903-0.24770.1025-0.0159-0.02120.03670.06460.0026-0.06910.129-0.1188-0.04550.1420.02940.050210.338-22.23150.778
41.30080.4369-0.6810.49140.00221.4245-0.0179-0.0697-0.00960.1077-0.0257-0.03170.0149-0.03240.04370.0914-0.0204-0.04940.0810.00960.041725.798-4.91738.817
50.517-0.60040.28493.3829-3.1593.2477-0.0090.2026-0.1029-0.22480.0210.07890.3325-0.1678-0.0120.1525-0.1043-0.05220.18720.02460.07897.851-23.09741.565
63.0954-1.6053-0.9073.93512.4314.3505-0.00050.1636-0.05520.4269-0.21550.19970.1112-0.61970.21590.0695-0.00410.02330.1892-0.05880.0253-14.32910.73335.986
72.79773.16330.4456.6607-0.19233.70350.33540.231-0.10260.50070.18991.09860.4322-0.1655-0.52530.20080.01890.03290.5683-0.1060.5185-22.8614.86933.125
82.3808-2.97240.15825.3164-0.01262.06220.1840.545-0.1003-0.3367-0.27080.25680.1562-0.39940.08680.13560.0835-0.06350.5068-0.03520.0599-14.7414.72420.3
91.0643-0.2197-0.76570.1530.12631.10110.0440.04590.0504-0.0733-0.040.0216-0.0647-0.2101-0.00410.1092-0.0006-0.05870.14050.01040.03917.20610.29619.251
107.33720.9084-0.84050.899-1.17911.57510.06160.08880.4920.2277-0.05930.0194-0.33260.0621-0.00240.18080.0739-0.02980.0835-0.00070.0546-4.42224.33627.98
113.11210.1844-1.1892.5171-2.39832.78150.0274-0.08390.0356-0.0635-0.2077-0.16430.01980.42180.18040.133-0.0723-0.07920.27960.0720.087446.8516.73218.493
122.5296-0.50230.05912.21460.14354.0154-0.0793-0.05250.10070.0436-0.1497-0.1188-0.15450.50710.2290.0774-0.0755-0.06350.12480.07590.058850.51918.17122.365
135.40991.3003-0.88410.3607-0.26780.21580.0119-0.28580.32110.1191-0.03550.0342-0.15160.03150.02360.3799-0.0391-0.08650.1824-0.04520.227631.91423.58730.413
141.3860.3315-0.55550.3498-0.1250.6694-0.0475-0.03650.030.15310.0088-0.0452-0.0337-0.04180.03870.1318-0.0008-0.05650.097-0.01610.035225.87311.96834.393
158.48515.06462.60853.3011-0.104111.4436-0.2143-0.40130.4126-0.0094-0.09390.176-0.9078-1.15250.30830.18390.1191-0.01360.1328-0.00940.136735.07929.91123.776
164.4552-1.5001-0.35211.60490.78931.9290.0984-0.03720.5236-0.0444-0.0235-0.48950.01130.2492-0.0750.063-0.02820.01290.11920.02930.168740.96-10.7523.737
177.77860.81790.84996.75030.37425.95860.15610.20160.6165-0.33320.2177-0.4456-0.56030.0922-0.37390.077-0.00080.08460.09880.03580.135740.983-5.305-5.705
183.1618-1.9234-1.01771.94641.75442.37330.17570.1755-0.1079-0.0665-0.15030.1069-0.0618-0.0488-0.02540.07740.0076-0.0030.0573-0.01870.059129.973-18.045-2.54
191.0835-0.3298-0.48250.23270.38541.31240.0193-0.0119-0.03360.0159-0.02760.00430.0792-0.05730.00830.0922-0.0662-0.040.06910.01490.030317.907-12.43315.631
200.6809-0.399-2.29683.61222.43148.2648-0.1016-0.0978-0.09610.3161-0.0506-0.23790.55230.24980.15220.1570.0005-0.05720.06180.06260.098330.937-25.52812.93
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 34
2X-RAY DIFFRACTION2A35 - 56
3X-RAY DIFFRACTION3A57 - 147
4X-RAY DIFFRACTION4A148 - 233
5X-RAY DIFFRACTION5A234 - 269
6X-RAY DIFFRACTION6B1 - 34
7X-RAY DIFFRACTION7B35 - 67
8X-RAY DIFFRACTION8B68 - 112
9X-RAY DIFFRACTION9B113 - 245
10X-RAY DIFFRACTION10B246 - 269
11X-RAY DIFFRACTION11C0 - 16
12X-RAY DIFFRACTION12C17 - 106
13X-RAY DIFFRACTION13C107 - 141
14X-RAY DIFFRACTION14C142 - 250
15X-RAY DIFFRACTION15C251 - 267
16X-RAY DIFFRACTION16D1 - 34
17X-RAY DIFFRACTION17D35 - 64
18X-RAY DIFFRACTION18D65 - 108
19X-RAY DIFFRACTION19D109 - 250
20X-RAY DIFFRACTION20D251 - 269

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