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- PDB-3ing: Crystal structure of Homoserine dehydrogenase (NP_394635.1) from ... -

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Basic information

Entry
Database: PDB / ID: 3ing
TitleCrystal structure of Homoserine dehydrogenase (NP_394635.1) from THERMOPLASMA ACIDOPHILUM at 1.95 A resolution
ComponentsHomoserine dehydrogenase
KeywordsOXIDOREDUCTASE / NP_394635.1 / Homoserine dehydrogenase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


homoserine dehydrogenase / homoserine dehydrogenase activity / threonine biosynthetic process / NADP binding
Similarity search - Function
Homoserine dehydrogenase lacking ACT domain / Homoserine dehydrogenase, conserved site / Homoserine dehydrogenase signature. / Homoserine dehydrogenase, catalytic / Homoserine dehydrogenase / Aspartate/homoserine dehydrogenase, NAD-binding / Homoserine dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain ...Homoserine dehydrogenase lacking ACT domain / Homoserine dehydrogenase, conserved site / Homoserine dehydrogenase signature. / Homoserine dehydrogenase, catalytic / Homoserine dehydrogenase / Aspartate/homoserine dehydrogenase, NAD-binding / Homoserine dehydrogenase, NAD binding domain / 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
Chem-NDP / Homoserine dehydrogenase
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Homoserine dehydrogenase (NP_394635.1) from THERMOPLASMA ACIDOPHILUM at 1.95 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Homoserine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2669
Polymers36,1251
Non-polymers1,1418
Water3,855214
1
A: Homoserine dehydrogenase
hetero molecules

A: Homoserine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,53218
Polymers72,2502
Non-polymers2,28216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area7420 Å2
ΔGint10 kcal/mol
Surface area23800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.821, 92.113, 120.788
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY PROVIDES SUPPORTING EVIDENCE THAT THE DIMER IS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Homoserine dehydrogenase /


Mass: 36125.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: NP_394635.1, Ta1179 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9HIZ7
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.69 Å3/Da / Density % sol: 54.24 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.14
Details: 49.0000% 2-propanol, 5.0000% polyethylene glycol 1000, 0.1M citric acid pH 5.14, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97927,0.97908
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 19, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979271
30.979081
ReflectionResolution: 1.95→28.105 Å / Num. obs: 28686 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.65 % / Biso Wilson estimate: 20.319 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 8.45
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.95-2.020.4991.6101885339197.2
2.02-2.10.3492.2102915375198.8
2.1-2.20.2613110215723199
2.2-2.310.2123.799295147198.9
2.31-2.460.1734.4107665592199.1
2.46-2.650.1325.8105105427198.9
2.65-2.910.0958103255308199
2.91-3.330.06211.6104905400198.5
3.33-4.190.03619.3105485407198.3
4.19-28.1050.02624.8105695418197.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→28.105 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 5.481 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.122
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS OTHER REFINEMENT REMARKS: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS OTHER REFINEMENT REMARKS: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NDP) AND SODIUM (NA), MOST LIKELY BOUND DURING PROTEIN EXPRESSION WERE MODELED INTO THE STRUCTURE. THE SODIUM WAS ASSIGNED BASED ON THE COORDINATION ENVIRONMENT, AGREEMENT WITH ELECTRON DENSITY AND IT STRUCTURAL HOMOLOG(PDB ID 1EBU). ETHYLENE GLYCOL (EDO) USED AS CRYOPROTECTANT WAS MODELED INTO THE STRUCTURE. 5.THE RAMACHANDRAN OUTLIER (GLY146) IS SUPPORTED BY ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.193 1435 5 %RANDOM
Rwork0.152 ---
obs0.154 28657 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 81.83 Å2 / Biso mean: 28.208 Å2 / Biso min: 6.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.99 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 1.95→28.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2405 0 73 214 2692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222589
X-RAY DIFFRACTIONr_bond_other_d0.0020.021704
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.9893517
X-RAY DIFFRACTIONr_angle_other_deg1.1234163
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.145335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.724.455110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.69215428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.331519
X-RAY DIFFRACTIONr_chiral_restr0.0780.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022916
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02499
X-RAY DIFFRACTIONr_nbd_refined0.2420.3536
X-RAY DIFFRACTIONr_nbd_other0.1970.31963
X-RAY DIFFRACTIONr_nbtor_refined0.1820.51306
X-RAY DIFFRACTIONr_nbtor_other0.0910.51324
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.5321
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0270.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.39
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3110.333
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.522
X-RAY DIFFRACTIONr_mcbond_it1.90931633
X-RAY DIFFRACTIONr_mcbond_other0.5433675
X-RAY DIFFRACTIONr_mcangle_it3.11352638
X-RAY DIFFRACTIONr_scbond_it4.9778977
X-RAY DIFFRACTIONr_scangle_it7.15911879
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 93 -
Rwork0.212 1990 -
all-2083 -
obs--98.21 %
Refinement TLS params.Method: refined / Origin x: 31.2118 Å / Origin y: 31.4842 Å / Origin z: 13.9403 Å
111213212223313233
T-0.0475 Å2-0.0017 Å2-0.0123 Å2--0.0398 Å20.0062 Å2---0.0482 Å2
L0.6958 °20.1058 °20.124 °2-0.7172 °2-0.0433 °2--0.7958 °2
S0.0193 Å °-0.0168 Å °-0.0511 Å °-0.0439 Å °-0.0056 Å °-0.0127 Å °0.0291 Å °-0.0293 Å °-0.0137 Å °

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