[English] 日本語
Yorodumi
- PDB-4pg7: Crystal structure of S. aureus Homoserine Dehydrogenase at pH7.5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pg7
TitleCrystal structure of S. aureus Homoserine Dehydrogenase at pH7.5
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 / LYSINE / DI(HYDROXYETHYL)ETHER / Homoserine dehydrogenase / :
Similarity search - Component
Biological speciesStaphylococcus aureus M1064 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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 / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Homoserine dehydrogenase
B: Homoserine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,14620
Polymers102,7682
Non-polymers1,37718
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-6 kcal/mol
Surface area36290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.040, 117.660, 119.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 2 - 426 / Label seq-ID: 22 - 446

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
Detailsbiological unit is the same as asym.

-
Components

-
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

-
Non-polymers , 5 types, 339 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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M Magnesium acetate, 18% PEG8000, 0.1M Tris-HCl, pH7.5, 5% Glycerol

-
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 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionRedundancy: 7.3 % / Number: 434637 / Rsym value: 0.057 / D res high: 2.1 Å / D res low: 119.48 Å / Num. obs: 59396 / % possible obs: 97.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRsym valueRedundancy
6.6434.9210.0210.0217.2
4.76.6410.0320.0327.8
3.834.710.0470.0477.9
3.323.8310.0530.0538
2.973.3210.0580.0587.8
2.712.9710.0830.0837.4
2.512.7110.130.137
2.352.5110.2040.2046.9
2.212.3510.2940.2946.9
2.12.2110.4380.4387
ReflectionResolution: 2.1→119.48 Å / Num. all: 59396 / Num. obs: 59396 / % possible obs: 97.8 % / Observed criterion σ(F): 3 / Redundancy: 7.3 % / Biso Wilson estimate: 44.8 Å2 / Rpim(I) all: 0.022 / Rrim(I) all: 0.062 / Rsym value: 0.057 / Net I/av σ(I): 8.699 / Net I/σ(I): 19 / Num. measured all: 434637
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
2.1-2.2170.4381.85696281410.1730.4384.193.4
2.21-2.356.90.2942.65447778720.1170.294695
2.35-2.516.90.2043.75204175420.0820.2048.696.8
2.51-2.7170.135.75063672310.0520.1312.799.3
2.71-2.977.40.0838.54947267170.0330.08318.6100
2.97-3.327.80.05811.34807561390.0220.05825.7100
3.32-3.8380.05311.14330854320.020.05333.8100
3.83-4.77.90.04712.23653846200.0170.04740.1100
4.7-6.647.80.03215.72832336490.0120.03241.2100
6.64-34.9257.20.02125.81480520530.0080.02142.697.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 45.13 / Model details: Phaser MODE: MR_AUTO

-
Processing

Software
NameClassification
HKL-3000data collection
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
Cootmodel building
REFMACrefinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→34.9 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.2287 / WRfactor Rwork: 0.1984 / FOM work R set: 0.8575 / SU B: 8.183 / SU ML: 0.111 / SU R Cruickshank DPI: 0.1897 / SU Rfree: 0.1627 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2253 2993 5 %RANDOM
Rwork0.1949 56338 --
obs0.1964 59331 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.33 Å2 / Biso mean: 32.862 Å2 / Biso min: 14.67 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å20 Å2-0 Å2
2--1.31 Å2-0 Å2
3----0.22 Å2
Refinement stepCycle: final / Resolution: 2.1→34.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5874 0 98 321 6293
Biso mean--57.54 44.87 -
Num. residues----790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196069
X-RAY DIFFRACTIONr_bond_other_d0.0040.025874
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.9738197
X-RAY DIFFRACTIONr_angle_other_deg0.919313459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7535792
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.38225.926243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67151027
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8411517
X-RAY DIFFRACTIONr_chiral_restr0.0710.2990
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026876
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021251
X-RAY DIFFRACTIONr_mcbond_it1.9713.2993179
X-RAY DIFFRACTIONr_mcbond_other1.9713.2993178
X-RAY DIFFRACTIONr_mcangle_it3.1854.9013942
Refine LS restraints NCS

Ens-ID: 1 / Number: 21514 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 200 -
Rwork0.23 3891 -
all-4091 -
obs--92.56 %
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)
10.8220.4744-0.43030.8877-0.50860.6414-0.10340.0810.155-0.14550.06050.08250.0179-0.03550.04290.0546-0.0396-0.03890.06430.00120.0828-28.413930.4329-22.9131
20.58570.04960.82060.33140.24311.6369-0.07490.0477-0.0291-0.07080.01130.0775-0.05320.06180.06360.0621-0.04320.02290.0567-0.03530.0522-7.96858.0235-30.5624
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 426
2X-RAY DIFFRACTION2B2 - 427

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more