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- PDB-3ivt: Homocitrate Synthase Lys4 bound to 2-OG -

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Basic information

Entry
Database: PDB / ID: 3ivt
TitleHomocitrate Synthase Lys4 bound to 2-OG
ComponentsHomocitrate synthase, mitochondrial
KeywordsTRANSFERASE / TIM barrel / Metalloprotein / Claisen condensation / Amino-acid biosynthesis / Lysine biosynthesis / Mitochondrion / Transit peptide
Function / homology
Function and homology information


homocitrate synthase / homocitrate synthase activity / lysine biosynthetic process / lysine biosynthetic process via aminoadipic acid / mitochondrion / metal ion binding / nucleus / cytosol
Similarity search - Function
Recoverin; domain 1 - #260 / : / Homocitrate synthase, fungi/archaea / Alpha-isopropylmalate and homocitrate synthases signature 2. / Alpha-isopropylmalate and homocitrate synthases signature 1. / Alpha-isopropylmalate/homocitrate synthase, conserved site / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Recoverin; domain 1 ...Recoverin; domain 1 - #260 / : / Homocitrate synthase, fungi/archaea / Alpha-isopropylmalate and homocitrate synthases signature 2. / Alpha-isopropylmalate and homocitrate synthases signature 1. / Alpha-isopropylmalate/homocitrate synthase, conserved site / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Recoverin; domain 1 / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / Homocitrate synthase, mitochondrial
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.67 Å
AuthorsBulfer, S.L. / Scott, E.M. / Couture, J.-F. / Pillus, L. / Trievel, R.C.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Crystal structure and functional analysis of homocitrate synthase, an essential enzyme in lysine biosynthesis.
Authors: Bulfer, S.L. / Scott, E.M. / Couture, J.F. / Pillus, L. / Trievel, R.C.
History
DepositionSep 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Homocitrate synthase, mitochondrial
B: Homocitrate synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9798
Polymers93,5102
Non-polymers4696
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11870 Å2
ΔGint-123 kcal/mol
Surface area28390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.731, 133.731, 125.904
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-501-

NA

21B-501-

NA

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Components

#1: Protein Homocitrate synthase, mitochondrial /


Mass: 46754.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: lys4, SPBC1105.02c / Plasmid: PHIS2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21DE3 / References: UniProt: Q9Y823, homocitrate synthase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 3.48 Å3/Da / Density % sol: 64.61 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: Na/KPO4, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 13, 2008
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.67→40 Å / Num. all: 36145 / Num. obs: 36145 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Χ2: 1.072 / Net I/σ(I): 16.8
Reflection shellResolution: 2.67→2.78 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 4.54 / Num. unique all: 3613 / Χ2: 1.193 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homocitrate Synthase Lys4

Resolution: 2.67→39.47 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 15.545 / SU ML: 0.162 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.377 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1795 5 %RANDOM
Rwork0.165 ---
all0.167 36145 --
obs0.167 36061 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.45 Å2 / Biso mean: 55.696 Å2 / Biso min: 25.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.02 Å20 Å2
2--0.03 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.67→39.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6078 0 24 151 6253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226289
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.9558536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0975818
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.52324285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.219151029
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8991546
X-RAY DIFFRACTIONr_chiral_restr0.0960.2999
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024768
X-RAY DIFFRACTIONr_nbd_refined0.2150.22941
X-RAY DIFFRACTIONr_nbtor_refined0.3070.24440
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2287
X-RAY DIFFRACTIONr_metal_ion_refined0.0490.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.26
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.10.21
X-RAY DIFFRACTIONr_mcbond_it0.551.54004
X-RAY DIFFRACTIONr_mcangle_it1.12426436
X-RAY DIFFRACTIONr_scbond_it2.07732324
X-RAY DIFFRACTIONr_scangle_it3.4894.52091
LS refinement shellResolution: 2.673→2.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 115 -
Rwork0.276 2464 -
all-2579 -
obs--96.41 %
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)
10.9244-0.25580.2241.8472-0.59541.7841-0.0502-0.1061-0.0020.2361-0.0840.069-0.1446-0.0710.1342-0.0664-0.06820.087-0.10250.0507-0.0793-25.248740.678116.8576
23.23260.9966-0.662.72760.52623.372-0.20990.1318-0.3762-0.1651-0.0305-0.4070.33550.41640.2404-0.14950.0140.14640.05890.14920.0049-1.607429.8093-2.6057
31.3711-0.4439-0.40781.13490.38771.7536-0.02340.21740.0596-0.1184-0.1044-0.042-0.1402-0.07620.1278-0.1435-0.01790.0855-0.02160.0459-0.0785-22.701942.4186-16.8754
42.92920.0150.04912.5852-0.75323.7644-0.1275-0.1398-0.39720.0755-0.066-0.09380.6273-0.04830.19350.0258-0.10160.2125-0.12850.04810.0022-24.876516.02192.2312
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 300
2X-RAY DIFFRACTION2A301 - 404
3X-RAY DIFFRACTION3B1 - 300
4X-RAY DIFFRACTION4B301 - 405

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