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- PDB-4pg4: Crystal structure of S. aureus Homoserine Dehydrogenase at pH6.0 -

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Basic information

Entry
Database: PDB / ID: 4pg4
TitleCrystal structure of S. aureus Homoserine Dehydrogenase at pH6.0
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 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: Advisory / Author supporting evidence ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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)104,52327
Polymers102,7682
Non-polymers1,75525
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-0 kcal/mol
Surface area35440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.460, 116.320, 118.350
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: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 1 - 427 / Label seq-ID: 21 - 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, 280 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 17 / 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.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 0.2M Magnesium acetate, 22% PEG8000, 0.1M Bis-Tris, pH6.0, 5% Glycerol, 1mM Serine

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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: 8.2 % / Number: 411942 / Rsym value: 0.071 / D res high: 2.2 Å / D res low: 118.35 Å / Num. obs: 50394 / % possible obs: 98
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRsym valueRedundancy
6.9639.4510.0290.0297.7
4.926.9610.0510.0518.3
4.024.9210.0630.0638.5
3.484.0210.060.068.5
3.113.4810.0670.0678.5
2.843.1110.0880.0888.3
2.632.8410.1320.1328
2.462.6310.1970.1978
2.322.4610.2990.2998
2.22.3210.4350.4358
ReflectionResolution: 2.2→118.35 Å / Num. obs: 50394 / % possible obs: 98 % / Redundancy: 8.2 % / Biso Wilson estimate: 47.8 Å2 / Rsym value: 0.071 / Net I/σ(I): 16.8
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
2.2-2.3280.4351.85571669570.1560.4354.894.1
2.32-2.4680.2992.55297666430.1080.2996.495.1
2.46-2.6380.1973.95112364260.0710.1978.997.3
2.63-2.8480.1325.64907661210.0480.13212.699.5
2.84-3.118.30.08884714656930.0320.08817.599.9
3.11-3.488.50.0679.94412451900.0240.06723100
3.48-4.028.50.0610.33934846050.0220.0628.7100
4.02-4.928.50.0639.63323139240.0230.06332.8100
4.92-6.968.30.05111.32573430930.0190.05131.8100
6.96-39.457.70.02920.81346817420.0110.02934.597.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.2 Å37.36 Å
Translation2.2 Å37.36 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-3000data collection
SCALA3.3.21data scaling
PHASER2.5.1phasing
Cootmodel building
PDB_EXTRACT3.14data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DO5

3do5


Resolution: 2.2→39.5 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.836 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2556 5.1 %RANDOM
Rwork0.2 ---
obs0.202 47777 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.59 Å2
Baniso -1Baniso -2Baniso -3
1--1.34 Å20 Å20 Å2
2--1.84 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5770 0 115 255 6140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195968
X-RAY DIFFRACTIONr_bond_other_d0.0040.025779
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.9768061
X-RAY DIFFRACTIONr_angle_other_deg0.938313214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0575781
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.88225.751233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20815999
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9491519
X-RAY DIFFRACTIONr_chiral_restr0.0730.2980
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026764
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021223
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_it2.2243.4843135
X-RAY DIFFRACTIONr_mcbond_other2.2013.473117
X-RAY DIFFRACTIONr_mcangle_it3.5415.1773883
X-RAY DIFFRACTIONr_mcangle_other3.5415.1783884
X-RAY DIFFRACTIONr_scbond_it2.573.612833
X-RAY DIFFRACTIONr_scbond_other2.573.6112834
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0175.3164173
X-RAY DIFFRACTIONr_long_range_B_refined6.60727.2296655
X-RAY DIFFRACTIONr_long_range_B_other6.60627.2346656
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 21343 / 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
Rfree0.263 192 -
Rwork0.216 3290 -
obs--93.33 %
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)
11.010.6081-0.56210.7699-0.56840.6611-0.11930.09630.1868-0.10390.08860.08990.0226-0.07640.03070.0515-0.0331-0.04620.04490.00050.10787.7983-28.212-22.4222
20.53630.10710.8030.31250.151.8811-0.07760.0544-0.0214-0.06340.01680.0701-0.08450.09340.06080.04-0.03770.01220.0503-0.02480.048328.1971-50.2932-30.5481
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 427
2X-RAY DIFFRACTION2B1 - 427

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