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

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Basic information

Entry
Database: PDB / ID: 5vlc
TitleCrystal Structure of Medicago truncatula L-Histidinol Dehydrogenase in Complex with L-Histidinol
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
L-histidinol / Histidinol dehydrogenase, chloroplastic
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)290,40818
Polymers289,1626
Non-polymers1,24612
Water11,259625
1
A: Histidinol dehydrogenase, chloroplastic
B: Histidinol dehydrogenase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8036
Polymers96,3872
Non-polymers4154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11760 Å2
ΔGint-133 kcal/mol
Surface area30760 Å2
MethodPISA
2
C: Histidinol dehydrogenase, chloroplastic
D: Histidinol dehydrogenase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8036
Polymers96,3872
Non-polymers4154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11870 Å2
ΔGint-131 kcal/mol
Surface area30040 Å2
MethodPISA
3
E: Histidinol dehydrogenase, chloroplastic
F: Histidinol dehydrogenase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8036
Polymers96,3872
Non-polymers4154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11970 Å2
ΔGint-132 kcal/mol
Surface area30670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.859, 139.201, 102.692
Angle α, β, γ (deg.)90.00, 119.18, 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) / Strain (production host): Gold / References: UniProt: G7IKX3, histidinol dehydrogenase
#2: Chemical
ChemComp-HSO / L-histidinol


Type: L-peptide linking / Mass: 142.179 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H12N3O
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 625 / 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: 2.22 Å3/Da / Density % sol: 44.59 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.2 / Details: 100 mM MES pH 5.2, 200 mM NACl, 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97625 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 17, 2016
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.97→48.73 Å / Num. obs: 175983 / % possible obs: 99.4 % / Redundancy: 6.14 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 13.7
Reflection shellResolution: 1.97→2.09 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.905 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 27746 / % possible all: 97.4

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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: 1.97→48.73 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 10.067 / SU ML: 0.133 / Cross valid method: FREE R-VALUE / ESU R: 0.165 / ESU R Free: 0.155 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22912 1232 0.7 %RANDOM
Rwork0.17853 ---
obs0.17888 174751 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.206 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å20.22 Å2
2---0.38 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.97→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19688 0 66 625 20379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01920189
X-RAY DIFFRACTIONr_bond_other_d0.0020.0219388
X-RAY DIFFRACTIONr_angle_refined_deg1.6931.95827386
X-RAY DIFFRACTIONr_angle_other_deg1.0142.99944768
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.32152586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00925.198810
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.111153368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8571569
X-RAY DIFFRACTIONr_chiral_restr0.1030.23181
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02122753
X-RAY DIFFRACTIONr_gen_planes_other00.024226
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_it1.7913.38110383
X-RAY DIFFRACTIONr_mcbond_other1.7913.38110384
X-RAY DIFFRACTIONr_mcangle_it2.8115.05812953
X-RAY DIFFRACTIONr_mcangle_other2.8115.05812954
X-RAY DIFFRACTIONr_scbond_it2.1673.7089806
X-RAY DIFFRACTIONr_scbond_other2.1673.7089807
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5365.44514433
X-RAY DIFFRACTIONr_long_range_B_refined5.51927.25222527
X-RAY DIFFRACTIONr_long_range_B_other5.49427.16922391
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.974→2.025 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 85 -
Rwork0.292 12173 -
obs--94.54 %
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)
10.5149-0.2594-0.41190.42030.22530.3320.07630.02570.0137-0.057-0.06070.0381-0.0568-0.0269-0.01560.04640.0131-0.02160.0720.00340.0753-14.70778.592-6.671
20.5747-0.231-0.38510.59180.19740.294-0.05910.0457-0.1439-0.0778-0.04930.11620.0090.00820.10840.0525-0.0074-0.01130.0905-0.02560.0707-7.0960.124-14.211
30.2542-0.09270.05590.245-0.05120.61960.0838-0.02570.0489-0.02750.0438-0.0638-0.1255-0.0426-0.12770.0664-0.02080.05340.0933-0.01980.068733.25278.03510.38
40.25440.0237-0.05260.4451-0.04550.45430.0631-0.0871-0.0566-0.02540.0692-0.1250.0654-0.0582-0.13230.0316-0.0323-0.03520.107-0.00050.1134.68458.52819.317
51.40610.73160.63980.95030.39580.4958-0.2305-0.22990.242-0.06260.03480.1736-0.02410.02740.19570.07390.0977-0.00560.14640.01720.0763-5.63175.51343.157
61.12330.33070.67440.5969-0.06130.7644-0.0951-0.2623-0.1952-0.13350.0775-0.03130.0859-0.13430.01760.06740.03280.07030.1530.1190.1284-13.25456.56838.254
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A42 - 475
2X-RAY DIFFRACTION2B42 - 473
3X-RAY DIFFRACTION3C42 - 475
4X-RAY DIFFRACTION4D42 - 473
5X-RAY DIFFRACTION5E42 - 475
6X-RAY DIFFRACTION6F42 - 475

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