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- PDB-4pg5: Crystal structure of S. aureus Homoserine Dehydrogenase at pH6.5 -

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Basic information

Entry
Database: PDB / ID: 4pg5
TitleCrystal structure of S. aureus Homoserine Dehydrogenase at pH6.5
ComponentsHomoserine dehydrogenase
KeywordsOXIDOREDUCTASE / Aspartic acid pathway / pH sensitivity / hydride transfer / ACT domain
Function / homology
Function and homology information


homoserine dehydrogenase / homoserine dehydrogenase activity / threonine biosynthetic process / methionine biosynthetic process / isoleucine biosynthetic process / NADP binding
Similarity search - Function
Alpha-Beta Plaits - #3100 / : / Homoserine dehydrogenase C-terminal domain / Homoserine dehydrogenase / Homoserine dehydrogenase, conserved site / Homoserine dehydrogenase signature. / Homoserine dehydrogenase, catalytic / Homoserine dehydrogenase / Aspartate/homoserine dehydrogenase, NAD-binding / Homoserine dehydrogenase, NAD binding domain ...Alpha-Beta Plaits - #3100 / : / Homoserine dehydrogenase C-terminal domain / Homoserine dehydrogenase / 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 / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / Homoserine dehydrogenase / :
Similarity search - Component
Biological speciesStaphylococcus aureus M1064 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
Model detailsStructure solved using the data obtained from the crystals grown at pH6.0 crystallization condition
AuthorsNavratna, V. / Gopal, B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural basis for the catalytic mechanism of homoserine dehydrogenase.
Authors: Navratna, V. / Reddy, G. / Gopal, B.
History
DepositionMay 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Jul 1, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Homoserine dehydrogenase
B: Homoserine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,12721
Polymers102,7682
Non-polymers1,35819
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-1 kcal/mol
Surface area36410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.480, 115.430, 118.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 3 - 427 / Label seq-ID: 23 - 447

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Homoserine dehydrogenase / HDH


Mass: 51384.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus M1064 (bacteria) / Gene: U5K_01898 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS
References: UniProt: N6FDB4, UniProt: A0A0M3KKV6*PLUS, homoserine dehydrogenase

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Non-polymers , 5 types, 255 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Magnesium acetate, 16% PEG3350, 0.1M Sodium Cacodylate, pH6.5, 5% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionRedundancy: 8.6 % / Number: 440598 / Rsym value: 0.065 / D res high: 2.2 Å / D res low: 118.23 Å / Num. obs: 51107 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRsym valueRedundancy
6.9638.4810.0230.0237.8
4.926.9610.0370.0378.4
4.024.9210.0540.0548.6
3.484.0210.0570.0578.7
3.113.4810.0570.0578.7
2.843.1110.0790.0798.7
2.632.8410.1290.1298.7
2.462.6310.20.28.7
2.322.4610.3170.3178.6
2.22.3210.4920.4928.5
ReflectionResolution: 2.2→118.23 Å / Num. obs: 51107 / % possible obs: 100 % / Redundancy: 8.6 % / Biso Wilson estimate: 48.4 Å2 / Net I/σ(I): 20.7
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.2-2.328.50.4921.16254473400.1770.4924.8100
2.32-2.468.60.3172.46024269670.1130.3176.7100
2.46-2.638.70.23.85724665680.0710.210.1100
2.63-2.848.70.1295.65354261270.0460.12915.1100
2.84-3.118.70.0799.14959456750.0280.07921.5100
3.11-3.488.70.05710.64465351370.0210.05728.7100
3.48-4.028.70.0579.73962545760.0210.05736.4100
4.02-4.928.60.05410.43330138720.0190.05442.2100
4.92-6.968.40.03714.42594530730.0140.03743.3100
6.96-38.4777.80.02322.11390617720.0090.0234899.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.2 Å37.3 Å
Translation2.2 Å37.3 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-3000data collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DO5

3do5


Resolution: 2.2→38.5 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.932 / SU B: 10.077 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2588 5.1 %RANDOM
Rwork0.201 ---
obs0.203 48454 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.28 Å2
Baniso -1Baniso -2Baniso -3
1--1.34 Å20 Å20 Å2
2--1.66 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5822 0 86 236 6144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195980
X-RAY DIFFRACTIONr_bond_other_d0.0040.025743
X-RAY DIFFRACTIONr_angle_refined_deg1.3621.9738074
X-RAY DIFFRACTIONr_angle_other_deg0.952313135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.245783
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.44525.751233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.50715996
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8271518
X-RAY DIFFRACTIONr_chiral_restr0.0780.2982
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026764
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021222
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_it2.3383.7213166
X-RAY DIFFRACTIONr_mcbond_other2.3233.7143154
X-RAY DIFFRACTIONr_mcangle_it3.7165.5253918
X-RAY DIFFRACTIONr_mcangle_other3.7165.5263919
X-RAY DIFFRACTIONr_scbond_it2.5653.7782814
X-RAY DIFFRACTIONr_scbond_other2.5643.782815
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.975.5914153
X-RAY DIFFRACTIONr_long_range_B_refined6.58928.8586658
X-RAY DIFFRACTIONr_long_range_B_other6.59328.8636659
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 20980 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 186 -
Rwork0.245 3497 -
obs--100 %
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)
11.23220.6761-0.65020.8501-0.59750.6749-0.13580.14240.2704-0.11490.10580.09490.0475-0.10470.030.034-0.0266-0.05360.04490.01070.16467.5539-28.0902-22.1116
20.48930.10140.75910.25070.0842.0645-0.07030.0512-0.0006-0.03860.00380.0593-0.12050.12190.06650.0368-0.03380.01490.0366-0.02330.046328.2712-49.3849-30.6431
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 427
2X-RAY DIFFRACTION2B1 - 427

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