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

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Basic information

Entry
Database: PDB / ID: 3ivu
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 / mitochondrial matrix / metal ion binding / nucleus / cytosol
Similarity search - Function
: / Homocitrate synthase, fungi/archaea / : / Homocitrate synthase post-HMGL domain-like / Alpha-isopropylmalate and homocitrate synthases signature 2. / : / Alpha-isopropylmalate and homocitrate synthases signature 1. / Alpha-isopropylmalate/homocitrate synthase, conserved site / Pyruvate carboxyltransferase / HMGL-like ...: / Homocitrate synthase, fungi/archaea / : / Homocitrate synthase post-HMGL domain-like / 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. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / 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: 2.72 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)93,9668
Polymers93,5102
Non-polymers4566
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10060 Å2
ΔGint-72 kcal/mol
Surface area28110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.798, 133.798, 125.657
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-503-

NA

21B-503-

NA

Detailsbiological unit is the same as asym.

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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-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#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


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


Mass: 18.015 Da / Num. of mol.: 117 / 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: 3.47 Å3/Da / Density % sol: 64.58 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Na/KPO4, pH 6.0, 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: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 8, 2007
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.72→40 Å / Num. all: 33176 / Num. obs: 33176 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.056 / Χ2: 1.075 / Net I/σ(I): 12.3
Reflection shellResolution: 2.72→2.82 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 2.54 / Num. unique all: 3362 / Χ2: 1.031 / % possible all: 98.5

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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: 2.72→39.41 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 18.229 / SU ML: 0.184 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.435 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1681 5.1 %RANDOM
Rwork0.177 ---
all0.18 33176 --
obs0.18 33172 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.85 Å2 / Biso mean: 66.186 Å2 / Biso min: 37.31 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å2-0.5 Å20 Å2
2---1.01 Å20 Å2
3---1.51 Å2
Refinement stepCycle: LAST / Resolution: 2.72→39.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5771 0 24 117 5912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225917
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.9568029
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1115775
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13724.16250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.76415928
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2611536
X-RAY DIFFRACTIONr_chiral_restr0.0990.2959
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024442
X-RAY DIFFRACTIONr_nbd_refined0.2240.22808
X-RAY DIFFRACTIONr_nbtor_refined0.3090.24178
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2265
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.26
X-RAY DIFFRACTIONr_mcbond_it0.5351.53846
X-RAY DIFFRACTIONr_mcangle_it1.0726137
X-RAY DIFFRACTIONr_scbond_it1.89932106
X-RAY DIFFRACTIONr_scangle_it3.1834.51887
LS refinement shellResolution: 2.716→2.787 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 116 -
Rwork0.212 2320 -
all-2436 -
obs--94.97 %
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)
10.7625-0.2610.14831.7987-0.48191.6663-0.0178-0.177-0.09550.2724-0.0740.0483-0.0874-0.0790.0918-0.086-0.07150.074-0.09320.0738-0.0932-25.210340.491217.1411
23.7037-1.0306-0.36755.01931.14793.1482-0.06540.073-0.3708-0.0748-0.1906-0.45070.35010.33330.256-0.19330.01770.14470.03680.15790.0253-1.314128.6089-1.2183
31.4379-0.6784-0.47471.21640.33511.6894-0.01010.26730.0307-0.1404-0.0687-0.1021-0.1366-0.0580.0788-0.1367-0.02560.0989-0.00950.0244-0.0733-22.436542.0735-17.1236
43.7001-0.74290.67383.8043-0.71133.1983-0.1274-0.1458-0.56190.0597-0.0859-0.03980.4939-0.0120.2134-0.0325-0.08910.2026-0.1680.04110.0362-24.282515.41371.7215
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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