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

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Basic information

Entry
Database: PDB / ID: 5vlb
TitleCrystal Structure of Medicago truncatula L-Histidinol Dehydrogenase in Complex with Imidazole
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
IMIDAZOLE / DI(HYDROXYETHYL)ETHER / Histidinol dehydrogenase, chloroplastic
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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
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_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.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.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

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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)290,60624
Polymers289,1626
Non-polymers1,44418
Water11,800655
1
A: Histidinol dehydrogenase, chloroplastic
B: Histidinol dehydrogenase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8698
Polymers96,3872
Non-polymers4816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11930 Å2
ΔGint-120 kcal/mol
Surface area32050 Å2
MethodPISA
2
C: Histidinol dehydrogenase, chloroplastic
D: Histidinol dehydrogenase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8698
Polymers96,3872
Non-polymers4816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12070 Å2
ΔGint-121 kcal/mol
Surface area31830 Å2
MethodPISA
3
E: Histidinol dehydrogenase, chloroplastic
F: Histidinol dehydrogenase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8698
Polymers96,3872
Non-polymers4816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12040 Å2
ΔGint-119 kcal/mol
Surface area32230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.752, 142.814, 105.357
Angle α, β, γ (deg.)90.00, 120.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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) / Variant (production host): Gold / References: UniProt: G7IKX3, histidinol dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 655 / 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: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Molecular Dimensions Morpheus Condition H1: 0.1 M Amino acids, 0.1 M Buffer System 1 pH 6.5, 50 % v/v Precipitant Mix 1

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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: Jun 12, 2015
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→38.52 Å / Num. obs: 120737 / % possible obs: 94.7 % / Redundancy: 5.15 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 15.7
Reflection shellResolution: 2.25→2.39 Å / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 2.06 / Num. unique obs: 15117 / % possible all: 73.8

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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: 2.25→38.52 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / SU B: 15.151 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.307 / ESU R Free: 0.223 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23388 1208 1 %RANDOM
Rwork0.18106 ---
obs0.18159 119527 94.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.071 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å2-0.35 Å2
2--0.63 Å20 Å2
3----0.39 Å2
Refinement stepCycle: 1 / Resolution: 2.25→38.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19734 0 78 656 20468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01920230
X-RAY DIFFRACTIONr_bond_other_d0.0020.0219443
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.96627426
X-RAY DIFFRACTIONr_angle_other_deg1.022344892
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.38452592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5925.16814
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.819153381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8141571
X-RAY DIFFRACTIONr_chiral_restr0.0980.23182
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02122819
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024260
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_it1.4743.14410386
X-RAY DIFFRACTIONr_mcbond_other1.4743.14310385
X-RAY DIFFRACTIONr_mcangle_it2.4074.70712972
X-RAY DIFFRACTIONr_mcangle_other2.4074.70812973
X-RAY DIFFRACTIONr_scbond_it1.7813.4549844
X-RAY DIFFRACTIONr_scbond_other1.7813.4549844
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9935.06414455
X-RAY DIFFRACTIONr_long_range_B_refined4.69425.12122411
X-RAY DIFFRACTIONr_long_range_B_other4.69325.12322412
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.255→2.313 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 43 -
Rwork0.352 4234 -
obs--46.07 %
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)
10.4055-0.2457-0.28030.46850.15560.25060.0418-0.01140.0545-0.09160.01860.0406-0.0356-0.0151-0.06040.06140.0033-0.01920.010.01060.0974-14.165680.5119-7.9388
20.434-0.2655-0.16610.44020.00430.1233-0.0289-0.0347-0.0689-0.08880.02630.06920.02310.02750.00260.0809-0.0119-0.01430.0136-0.01050.0826-6.416761.6588-12.3289
30.33430.15280.41850.3476-0.08340.8961-0.14020.06020.0124-0.03630.1047-0.0944-0.1642-0.0190.03550.0717-0.023-0.03880.0366-0.01590.096635.014880.032510.8123
40.22390.03790.31770.2919-0.21491.1949-0.06-0.027-0.0403-0.00160.111-0.16180.1133-0.164-0.0510.10010.004-0.05130.0518-0.05440.130233.681261.379521.3748
50.33930.2591-0.01160.36650.15090.353-0.0014-0.00810.04080.06480.05080.0817-0.01860.1397-0.04940.0766-0.01460.0490.0562-0.02160.0679-6.809382.133343.4677
60.28460.29890.09650.4430.15050.45020.01170.026-0.03860.09380.04720.03990.07440.051-0.05880.0650.01020.03350.01370.00850.0767-14.402562.795339.0743
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 476
2X-RAY DIFFRACTION2B43 - 476
3X-RAY DIFFRACTION3C43 - 472
4X-RAY DIFFRACTION4D43 - 475
5X-RAY DIFFRACTION5E43 - 475
6X-RAY DIFFRACTION6F43 - 475

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