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- PDB-6an0: Crystal Structure of Histidinol Dehydrogenase from Elizabethkingi... -

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Basic information

Entry
Database: PDB / ID: 6an0
TitleCrystal Structure of Histidinol Dehydrogenase from Elizabethkingia anophelis
ComponentsHistidinol dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / Elizabethkingia anophelis NUHP1 / dehydrogenase / hisD / zinc binding / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


histidinol dehydrogenase / histidinol dehydrogenase activity / L-histidine biosynthetic process / NAD binding / zinc ion binding
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 / IODIDE ION / Histidinol dehydrogenase
Similarity search - Component
Biological speciesElizabethkingia anophelis NUHP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal Structure of Histidinol Dehydrogenase from Elizabethkingia anophelis
Authors: Dranow, D.M. / Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionAug 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 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_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_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_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_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histidinol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,09921
Polymers48,9171
Non-polymers2,18220
Water5,819323
1
A: Histidinol dehydrogenase
hetero molecules

A: Histidinol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,19842
Polymers97,8352
Non-polymers4,36340
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area16450 Å2
ΔGint-104 kcal/mol
Surface area31830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.520, 170.080, 65.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-861-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Histidinol dehydrogenase / HDH


Mass: 48917.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia anophelis NUHP1 (bacteria)
Strain: NUHP1 / Gene: hisD, BD94_1332 / Plasmid: ElanA.18181.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A077ECF2, histidinol dehydrogenase

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Non-polymers , 5 types, 343 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 1:1 21.3 mg/mL ElanA.18181.a.B1.PW3826 to MCSG1(e7) (20% w/v PEG3350, 0.2 M ammonium iodide, cryoprotection: 20% ethylene glycol, Tray 292598e7, puck ffs7-3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 14, 2017 / Details: Beryllium Lenses
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.85→31.449 Å / Num. obs: 39779 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.501 % / Biso Wilson estimate: 26.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.059 / Χ2: 1.029 / Net I/σ(I): 17.95 / Num. measured all: 218830 / Scaling rejects: 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.85-1.95.5750.5363.0729110.8810.589100
1.9-1.955.5850.3964.1728400.9270.436100
1.95-2.015.5980.3035.3827680.9530.33399.9
2.01-2.075.5780.2287.0927040.9730.2599.9
2.07-2.145.6140.1779.0826030.9850.19599.8
2.14-2.215.5840.1411.2825270.9890.15499.8
2.21-2.295.5470.11613.2924330.9930.12799.8
2.29-2.395.5760.09715.9623470.9940.10699.9
2.39-2.495.5590.08317.8422680.9960.09199.7
2.49-2.625.5280.0720.421660.9960.07799.9
2.62-2.765.4820.06123.2220530.9970.06899.8
2.76-2.935.4850.05425.9719510.9980.05999.6
2.93-3.135.4330.04928.3618420.9970.05599.6
3.13-3.385.4040.04132.7517160.9980.04599.1
3.38-3.75.3460.03835.1715670.9980.04298.8
3.7-4.145.3010.03536.7414350.9980.03998.9
4.14-4.785.3540.03238.4512640.9990.03598.5
4.78-5.855.2930.03137.6910720.9990.03597.6
5.85-8.275.1710.0337.428420.9990.03396.1
8.27-31.4494.8020.02737.464700.9990.0392

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1K75

1k75


Resolution: 1.85→31.449 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.36
RfactorNum. reflection% reflection
Rfree0.1922 1970 4.95 %
Rwork0.1571 --
obs0.1588 39771 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 113.52 Å2 / Biso mean: 33.2508 Å2 / Biso min: 4.75 Å2
Refinement stepCycle: final / Resolution: 1.85→31.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3253 0 49 327 3629
Biso mean--54.78 41.44 -
Num. residues----433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063377
X-RAY DIFFRACTIONf_angle_d0.7764592
X-RAY DIFFRACTIONf_chiral_restr0.055544
X-RAY DIFFRACTIONf_plane_restr0.005598
X-RAY DIFFRACTIONf_dihedral_angle_d13.7642063
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.89630.27341440.213526562800100
1.8963-1.94760.25311440.199226812825100
1.9476-2.00490.25391260.188826972823100
2.0049-2.06960.2321430.173726792822100
2.0696-2.14350.21500.166426522802100
2.1435-2.22930.20741340.162126852819100
2.2293-2.33070.20781310.157626942825100
2.3307-2.45360.22371260.164927222848100
2.4536-2.60720.1991510.167426912842100
2.6072-2.80840.19061210.170927252846100
2.8084-3.09080.22751580.171526932851100
3.0908-3.53750.19681450.15822718286399
3.5375-4.45490.15081620.13052713287599
4.4549-31.45340.16091350.14132795293097
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)
11.1593-0.50861.02731.5338-1.54273.9652-0.1748-0.27970.45420.4076-0.02540.1914-0.4977-0.00870.20650.4812-0.0109-0.02840.399-0.26490.441818.494232.03074.1767
23.1947-0.9576-0.54542.05710.21291.26630.13210.45780.4723-0.3352-0.0304-0.1399-0.19770.0522-0.110.2639-0.05860.0570.24840.05850.228516.733737.2035-34.5677
35.60830.93020.61320.8111-0.03280.53610.18180.0689-0.44890.0142-0.0541-0.0880.190.1271-0.09380.26430.0289-0.01750.1771-0.050.19764.98956.8908-22.8526
41.3782-0.3038-0.53663.2439-0.63351.49570.00360.13590.1385-0.13210.0448-0.2377-0.03510.1802-0.04060.158-0.02360.02880.1984-0.00580.133214.927925.8868-29.9137
52.4648-1.93573.29392.596-3.34624.9205-0.0222-0.07640.10650.25340.0205-0.0801-0.19980.0512-0.02430.2204-0.00430.03060.1886-0.03570.174912.222727.3026-12.0625
62.68360.70760.70862.18270.05641.67830.0659-0.37340.06890.2429-0.0034-0.2573-0.05410.1425-0.06250.1997-0.0139-0.03850.2249-0.05190.184723.087820.29911.0463
72.8151-0.18320.96940.6570.01061.0350.0903-0.093-0.0890.02890.02050.09680.0637-0.1136-0.10840.2112-0.01020.01810.11390.02630.1444-8.108814.4296-16.7316
82.6572.72722.47544.0333.39053.85160.10520.2657-0.74262.77740.0096-0.33281.3708-0.1905-0.08210.95720.2103-0.11850.59750.07161.0227-3.17047.2963-23.8015
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 26 )A-4 - 26
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 75 )A27 - 75
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 117 )A76 - 117
4X-RAY DIFFRACTION4chain 'A' and (resid 118 through 209 )A118 - 209
5X-RAY DIFFRACTION5chain 'A' and (resid 210 through 244 )A210 - 244
6X-RAY DIFFRACTION6chain 'A' and (resid 245 through 342 )A245 - 342
7X-RAY DIFFRACTION7chain 'A' and (resid 343 through 428 )A343 - 428
8X-RAY DIFFRACTION8chain 'E' and (resid 1 through 1 )E1

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