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- PDB-4pg6: Crystal structure of S. aureus Homoserine Dehydrogenase at pH7.0 -

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Basic information

Entry
Database: PDB / ID: 4pg6
TitleCrystal structure of S. aureus Homoserine Dehydrogenase at pH7.0
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 / 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 (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 13, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Sep 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 1.3Sep 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)104,36524
Polymers102,7682
Non-polymers1,59722
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint4 kcal/mol
Surface area36130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.640, 116.880, 118.620
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 / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1LYSLYSAA2 - 42622 - 446
2METMETBB1 - 42621 - 446

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Homoserine dehydrogenase


Mass: 51384.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: hom, CH51_06975, JN533_07120, QT38_06630, SASCBU26_01217
Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: W8UB14, homoserine dehydrogenase

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Non-polymers , 5 types, 285 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.45 Å3/Da / Density % sol: 49.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M Magnesium acetate, 16% PEG3350, 0.1M HEPES, pH7.0, 5%Glycerol, 20% Iso-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionRedundancy: 8.3 % / Number: 433739 / Rsym value: 0.075 / D res high: 2.2 Å / D res low: 118.62 Å / Num. obs: 52050 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRsym valueRedundancy
6.9634.7310.0360.0367.6
4.926.9610.0370.0378.1
4.024.9210.0640.0648.3
3.484.0210.0670.0678.3
3.113.4810.070.078.4
2.843.1110.0870.0878.4
2.632.8410.1370.1378.4
2.462.6310.2060.2068.4
2.322.4610.3160.3168.4
2.22.3210.4420.4428.4
ReflectionResolution: 2.2→118.62 Å / Num. obs: 52050 / % possible obs: 100 % / Redundancy: 8.3 % / Biso Wilson estimate: 47.2 Å2 / Net I/σ(I): 17.3
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
2.2-2.328.40.4421.76287374940.1620.4424.8100
2.32-2.468.40.3162.45949770830.1160.3166.6100
2.46-2.638.40.2063.65628166980.0750.2069.6100
2.63-2.848.40.1375.45245362510.050.13713.4100
2.84-3.118.40.0878.14827957580.0320.08718.4100
3.11-3.488.40.078.54390652440.0260.0723.6100
3.48-4.028.30.0678.33870546390.0240.06729.1100
4.02-4.928.30.0648.83276539610.0230.06433.5100
4.92-6.968.10.03712.92541031280.0140.03735.2100
6.96-34.7297.60.03610.31357017940.0130.03636.599.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.2 Å34.68 Å
Translation2.2 Å34.68 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-3000data collection
iMOSFLM3.3.21data reduction
SCALA2.5.1data scaling
PHASERphasing
Cootmodel building
PDB_EXTRACT3.14data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DO5

3do5


Resolution: 2.2→34.7 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / SU B: 9.992 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.244 2651 5.1 %RANDOM
Rwork0.203 ---
obs0.205 49330 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: 34.58 Å2
Baniso -1Baniso -2Baniso -3
1--1.32 Å20 Å20 Å2
2--2.08 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 2.2→34.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5787 0 103 263 6153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195973
X-RAY DIFFRACTIONr_bond_other_d0.0040.025782
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.9768061
X-RAY DIFFRACTIONr_angle_other_deg0.964313233
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2725781
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74925.87230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.399151008
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9061520
X-RAY DIFFRACTIONr_chiral_restr0.0750.2984
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026740
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021210
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_it2.2493.5153148
X-RAY DIFFRACTIONr_mcbond_other2.2353.5043134
X-RAY DIFFRACTIONr_mcangle_it3.5875.2233902
X-RAY DIFFRACTIONr_mcangle_other3.5885.2243903
X-RAY DIFFRACTIONr_scbond_it2.4223.6022825
X-RAY DIFFRACTIONr_scbond_other2.4223.6032826
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.855.3084157
X-RAY DIFFRACTIONr_long_range_B_refined6.46227.0836603
X-RAY DIFFRACTIONr_long_range_B_other6.46227.0896604
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 21352 / 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
Rfree0.243 195 -
Rwork0.218 3584 -
obs--99.97 %
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)
10.86160.5294-0.49990.8679-0.57940.5991-0.11680.05790.161-0.12560.06630.06590.037-0.04650.05050.06-0.0291-0.04520.0214-0.00390.1397.7406-28.2424-22.3645
20.45990.14180.72640.25320.22681.7376-0.08690.0505-0.0233-0.05790.00920.0722-0.08560.06290.07760.0386-0.02950.01880.0348-0.03210.073528.3162-50.243-30.6632
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 426
2X-RAY DIFFRACTION2B1 - 427

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