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- PDB-5vld: Crystal Structure of Medicago truncatula L-Histidinol Dehydrogena... -

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Basic information

Entry
Database: PDB / ID: 5vld
TitleCrystal Structure of Medicago truncatula L-Histidinol Dehydrogenase in Complex with L-Histidine and NAD+
ComponentsHistidinol dehydrogenase, chloroplastic
KeywordsOXIDOREDUCTASE / histidine biosynthesis / Zn2+ binding protein / NAD binding protein / plant protein
Function / homology
Function and homology information


histidinol dehydrogenase activity / L-histidine biosynthetic process / chloroplast / NAD binding / metal ion binding / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1300 / Histidinol dehydrogenase, conserved site / Histidinol dehydrogenase / Histidinol dehydrogenase, monofunctional / Histidinol dehydrogenase / Histidinol dehydrogenase signature. / Nitrogenase molybdenum iron protein domain / Aldehyde/histidinol dehydrogenase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1300 / Histidinol dehydrogenase, conserved site / Histidinol dehydrogenase / Histidinol dehydrogenase, monofunctional / Histidinol dehydrogenase / Histidinol dehydrogenase signature. / Nitrogenase molybdenum iron protein domain / Aldehyde/histidinol dehydrogenase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
HISTIDINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Histidinol dehydrogenase, chloroplastic
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsRuszkowski, M. / Dauter, Z.
CitationJournal: Sci Rep / Year: 2017
Title: Structures of Medicago truncatula L-Histidinol Dehydrogenase Show Rearrangements Required for NAD(+) Binding and the Cofactor Positioned to Accept a Hydride.
Authors: Ruszkowski, M. / Dauter, Z.
History
DepositionApr 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_seq_id / _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.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_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: Histidinol dehydrogenase, chloroplastic
B: Histidinol dehydrogenase, chloroplastic
C: Histidinol dehydrogenase, chloroplastic
D: Histidinol dehydrogenase, chloroplastic
E: Histidinol dehydrogenase, chloroplastic
F: Histidinol dehydrogenase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,68526
Polymers289,1626
Non-polymers5,52220
Water4,035224
1
A: Histidinol dehydrogenase, chloroplastic
B: Histidinol dehydrogenase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2649
Polymers96,3872
Non-polymers1,8767
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13330 Å2
ΔGint-154 kcal/mol
Surface area29980 Å2
MethodPISA
2
C: Histidinol dehydrogenase, chloroplastic
D: Histidinol dehydrogenase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1578
Polymers96,3872
Non-polymers1,7706
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13300 Å2
ΔGint-155 kcal/mol
Surface area29860 Å2
MethodPISA
3
E: Histidinol dehydrogenase, chloroplastic
F: Histidinol dehydrogenase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2649
Polymers96,3872
Non-polymers1,8767
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13540 Å2
ΔGint-151 kcal/mol
Surface area29870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.654, 139.095, 103.558
Angle α, β, γ (deg.)90.00, 119.47, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA42 - 47310 - 441
21ALAALABB42 - 47310 - 441
12GLUGLUAA42 - 47210 - 440
22GLUGLUCC42 - 47210 - 440
13ALAALAAA42 - 47310 - 441
23ALAALADD42 - 47310 - 441
14ALAALAAA42 - 47310 - 441
24ALAALAEE42 - 47310 - 441
15GLUGLUAA42 - 47210 - 440
25GLUGLUFF42 - 47210 - 440
16GLUGLUBB42 - 47210 - 440
26GLUGLUCC42 - 47210 - 440
17ALAALABB42 - 47310 - 441
27ALAALADD42 - 47310 - 441
18ALAALABB42 - 47310 - 441
28ALAALAEE42 - 47310 - 441
19ALAALABB42 - 47310 - 441
29ALAALAFF42 - 47310 - 441
110ILEILECC42 - 47110 - 439
210ILEILEDD42 - 47110 - 439
111ILEILECC42 - 47110 - 439
211ILEILEEE42 - 47110 - 439
112ILEILECC42 - 47110 - 439
212ILEILEFF42 - 47110 - 439
113GLUGLUDD42 - 47210 - 440
213GLUGLUEE42 - 47210 - 440
114ALAALADD42 - 47310 - 441
214ALAALAFF42 - 47310 - 441
115GLUGLUEE42 - 47210 - 440
215GLUGLUFF42 - 47210 - 440

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Histidinol dehydrogenase, chloroplastic / HDH


Mass: 48193.730 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: MTR_2g030520 / Production host: Escherichia coli (E. coli) / Strain (production host): Gold / References: UniProt: G7IKX3, histidinol dehydrogenase

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Non-polymers , 5 types, 244 molecules

#2: Chemical
ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H10N3O2
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.25 Å3/Da / Density % sol: 45.28 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.2 / Details: 100 mM MES pH 5.2, 200 mM NaCl, 10% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 7, 2017
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→48.89 Å / Num. obs: 76791 / % possible obs: 96.4 % / Redundancy: 2.85 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.3
Reflection shellResolution: 2.59→2.75 Å / Redundancy: 2.68 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 2.02 / Num. unique obs: 11619 / % possible all: 90.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XDSdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1kae

1kae


Resolution: 2.59→48.89 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.84 / SU B: 33.318 / SU ML: 0.33 / Cross valid method: FREE R-VALUE / ESU R Free: 0.36 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26437 1152 1.5 %RANDOM
Rwork0.22147 ---
obs0.22211 75639 96.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 56.791 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å2-0 Å2-0.36 Å2
2---0.92 Å20 Å2
3----0.27 Å2
Refinement stepCycle: 1 / Resolution: 2.59→48.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19659 0 350 224 20233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01920470
X-RAY DIFFRACTIONr_bond_other_d0.0090.0219507
X-RAY DIFFRACTIONr_angle_refined_deg1.741.97427818
X-RAY DIFFRACTIONr_angle_other_deg1.666345061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.78552584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.98625.148812
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.302153366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4261568
X-RAY DIFFRACTIONr_chiral_restr0.10.23228
X-RAY DIFFRACTIONr_gen_planes_refined00.02122906
X-RAY DIFFRACTIONr_gen_planes_other00.024308
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_it1.4232.56310372
X-RAY DIFFRACTIONr_mcbond_other1.4232.56310371
X-RAY DIFFRACTIONr_mcangle_it2.4743.83812941
X-RAY DIFFRACTIONr_mcangle_other2.4743.83812942
X-RAY DIFFRACTIONr_scbond_it1.2952.71610098
X-RAY DIFFRACTIONr_scbond_other1.2952.71610098
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2734.01914877
X-RAY DIFFRACTIONr_long_range_B_refined4.24519.98622248
X-RAY DIFFRACTIONr_long_range_B_other4.24519.98622248
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A508600.09
12B508600.09
21A513680.08
22C513680.08
31A515020.07
32D515020.07
41A519420.07
42E519420.07
51A520060.07
52F520060.07
61B508380.09
62C508380.09
71B509040.09
72D509040.09
81B512220.08
82E512220.08
91B512420.09
92F512420.09
101C515060.08
102D515060.08
111C518280.07
112E518280.07
121C517700.07
122F517700.07
131D515600.08
132E515600.08
141D518960.07
142F518960.07
151E521500.07
152F521500.07
LS refinement shellResolution: 2.59→2.657 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 71 -
Rwork0.316 4702 -
obs--82.01 %
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)
10.9049-0.4858-0.09970.84760.14810.07320.1866-0.16830.163-0.2522-0.15310.0203-0.0065-0.0265-0.03350.11110.0297-0.00520.1731-0.04560.2899-8.72379.785-12.892
20.8473-0.4491-0.05850.86420.10050.02970.0969-0.1064-0.0482-0.2159-0.10660.1182-0.01410.03210.00970.10850.0349-0.01210.172500.23491.72461.223-16.285
30.2224-0.274-0.14890.8696-0.46455.3210.3687-0.29090.0557-0.26740.7980.1185-0.86560.8165-1.16660.5169-0.45050.23020.9188-0.17410.287840.54382.8767.193
40.12260.0698-0.60161.1779-0.10373.213-0.0683-0.07710.10910.03490.7001-0.12290.54640.5812-0.63180.13680.1335-0.13230.5288-0.20310.188141.00163.70716.341
51.4002-0.00810.12660.52280.20530.1426-0.30910.0378-0.01930.09390.21820.0776-0.06010.09080.09090.2015-0.016-0.03450.19980.01430.16440.01581.1439.904
61.3020.03470.37280.6660.26350.3407-0.22320.1706-0.46210.10840.19060.0732-0.03290.05460.03260.0844-0.04210.05630.2012-0.03940.3285-7.25461.68134.49
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A42 - 473
2X-RAY DIFFRACTION2B42 - 473
3X-RAY DIFFRACTION3C42 - 472
4X-RAY DIFFRACTION4D42 - 474
5X-RAY DIFFRACTION5E42 - 473
6X-RAY DIFFRACTION6F42 - 476

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