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- PDB-3oq8: Crystal structure of isocitrate lyase from Brucella melitensis, b... -

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Basic information

Entry
Database: PDB / ID: 3oq8
TitleCrystal structure of isocitrate lyase from Brucella melitensis, bound to the product mimic malonate
ComponentsIsocitrate lyase
KeywordsLYASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


isocitrate lyase / isocitrate lyase activity / carboxylic acid metabolic process / metal ion binding
Similarity search - Function
Isocitrate lyase / Isocitrate lyase family / Isocitrate lyase/phosphorylmutase, conserved site / Isocitrate lyase signature. / ICL/PEPM domain / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
MALONIC ACID / Isocitrate lyase
Similarity search - Component
Biological speciesBrucella melitensis biovar Abortus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of isocitrate lyase from Brucella melitensis, bound to the product mimic malonate
Authors: SSGCID / Gardberg, A. / Edwards, T. / Staker, B. / Stewart, L.
History
DepositionSep 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 29, 2015Group: Non-polymer description
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isocitrate lyase
B: Isocitrate lyase
C: Isocitrate lyase
D: Isocitrate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,89828
Polymers188,5924
Non-polymers1,30624
Water21,2041177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31420 Å2
ΔGint-167 kcal/mol
Surface area48140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.500, 136.030, 181.770
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
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 4 / Auth seq-ID: 1 - 501 / Label seq-ID: 1 - 501

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
Isocitrate lyase /


Mass: 47148.051 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis biovar Abortus (bacteria)
Strain: 2308 / Gene: BAB1_1631 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2YQA0, isocitrate lyase
#2: Chemical
ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1177 / 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: 2.54 Å3/Da / Density % sol: 51.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Internal tracking number 217291H3. Hampton INDEX Screen condition H3: 0.2 M sodium malonate pH 7.0, 20% PEG3350, BrabA.00014.a.A1 PW 25251 at 26 mg/mL, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.25→39.2 Å / Num. all: 91893 / Num. obs: 91241 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 24.311 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.38
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.25-2.314.60.4794.2306346734668399.2
2.31-2.370.4124.431513654599.9
2.37-2.440.3544.830826635399.9
2.44-2.520.3964.828565616199.6
2.52-2.60.3175.528861599799.8
2.6-2.690.2546.228396580499.9
2.69-2.790.2386.6275415626100
2.79-2.90.2047.426430539699.9
2.9-3.030.1668.525705520999.9
3.03-3.180.1549.224436494399.8
3.18-3.350.14811.322199473799.4
3.35-3.560.09614.422143447399.6
3.56-3.80.07618.820749419599.2
3.8-4.110.0720.819538393899.1
4.11-4.50.06422.317909360298.9
4.5-5.030.06621.316176326498.3
5.03-5.810.08416.714439288898.2
5.81-7.120.09514.412287246497.3
7.12-10.060.05425.69187190196.3
10.06-39.20.04530.74833106290.7

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Phasing

Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å40.57 Å
Translation2.5 Å40.57 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EOL

3eol


Resolution: 2.25→39.2 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.922 / SU B: 10.272 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.199 4530 5 %RANDOM
Rwork0.149 ---
all0.151 91893 --
obs0.151 90916 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.324 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2--0.47 Å20 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 2.25→39.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12903 0 81 1177 14161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02213318
X-RAY DIFFRACTIONr_bond_other_d0.0010.028934
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.94818025
X-RAY DIFFRACTIONr_angle_other_deg0.951321684
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.01351710
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.48924.084622
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.625152116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4681584
X-RAY DIFFRACTIONr_chiral_restr0.0880.21936
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215250
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022798
X-RAY DIFFRACTIONr_mcbond_it0.6041.58430
X-RAY DIFFRACTIONr_mcbond_other0.2041.53474
X-RAY DIFFRACTIONr_mcangle_it1.108213329
X-RAY DIFFRACTIONr_scbond_it2.14534888
X-RAY DIFFRACTIONr_scangle_it3.4264.54685
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 5231 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
AMEDIUM POSITIONAL0.230.5
BMEDIUM POSITIONAL0.320.5
CMEDIUM POSITIONAL0.280.5
DMEDIUM POSITIONAL0.230.5
AMEDIUM THERMAL0.662
BMEDIUM THERMAL0.642
CMEDIUM THERMAL0.652
DMEDIUM THERMAL0.652
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 314 -
Rwork0.197 6331 -
all-6645 -
obs-6683 99.09 %
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)
10.1550.04390.06780.3177-0.1120.3474-0.0060.00640.0401-0.00190.0046-0.0106-0.0677-0.01560.00140.02810.0098-0.00230.0137-0.00680.029657.732166.35529.483
20.12720.05740.0090.3579-0.13530.43310.0043-0.023900.0389-0.0436-0.10390.00170.12090.03930.0068-0.0015-0.01810.05970.01550.055778.437148.11746.325
30.09310.0469-0.04810.2529-0.07350.4205-0.0021-0.0015-0.00440.01060.01370.03980.0573-0.0806-0.01160.0132-0.0191-0.00130.04110.00260.017743.829133.48243.379
40.13220.0487-0.07770.1925-0.13220.5203-0.02270.0393-0.0402-0.08130.0012-0.04450.11450.01720.02150.0710.00740.01670.0228-0.01390.019361.387131.41716.036
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 501
2X-RAY DIFFRACTION2B1 - 501
3X-RAY DIFFRACTION3C1 - 501
4X-RAY DIFFRACTION4D1 - 501

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