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- PDB-3m6y: Structure of 4-hydroxy-2-oxoglutarate aldolase from bacillus cere... -

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Basic information

Entry
Database: PDB / ID: 3m6y
TitleStructure of 4-hydroxy-2-oxoglutarate aldolase from bacillus cereus at 1.45 a resolution.
Components4-Hydroxy-2-oxoglutarate aldolase
KeywordsLYASE / STRUCTURAL GENOMICS / MCSG / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


4-hydroxy-2-oxoglutarate aldolase / (R,S)-4-hydroxy-2-oxoglutarate aldolase activity / metal ion binding
Similarity search - Function
2-dehydro-3-deoxy-phosphogluconate aldolase / KDGP aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
4-Hydroxy-2-oxoglutarate aldolase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsFilippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Clancy, S. / Joachimiak, A. / Anderson, F.W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of 4-Hydroxy-2-Oxoglutarate Aldolase from Bacillus Cereus at 1.45 A Resolution.
Authors: Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Clancy, S. / Joachimiak, A. / Anderson, W.F.
History
DepositionMar 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Nov 27, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_alt_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_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: 4-Hydroxy-2-oxoglutarate aldolase
B: 4-Hydroxy-2-oxoglutarate aldolase
C: 4-Hydroxy-2-oxoglutarate aldolase
D: 4-Hydroxy-2-oxoglutarate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,22114
Polymers119,8484
Non-polymers37310
Water21,7081205
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 4-Hydroxy-2-oxoglutarate aldolase
D: 4-Hydroxy-2-oxoglutarate aldolase
hetero molecules

B: 4-Hydroxy-2-oxoglutarate aldolase
C: 4-Hydroxy-2-oxoglutarate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,22114
Polymers119,8484
Non-polymers37310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y+1/2,-z1
Buried area5790 Å2
ΔGint-117 kcal/mol
Surface area37770 Å2
MethodPISA
3
A: 4-Hydroxy-2-oxoglutarate aldolase
D: 4-Hydroxy-2-oxoglutarate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1117
Polymers59,9242
Non-polymers1875
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-56 kcal/mol
Surface area19600 Å2
MethodPISA
4
B: 4-Hydroxy-2-oxoglutarate aldolase
C: 4-Hydroxy-2-oxoglutarate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1117
Polymers59,9242
Non-polymers1875
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-58 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.679, 106.187, 88.205
Angle α, β, γ (deg.)90.00, 90.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
4-Hydroxy-2-oxoglutarate aldolase


Mass: 29962.051 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / DSM 31 / Gene: 29898472, BC_4844 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Magic
References: UniProt: Q812M4, 4-hydroxy-2-oxoglutarate aldolase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1205 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.9 Å3/Da / Density % sol: 35.33 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M CaCl, 0.1 M HEPES, 30% PEG4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.987872
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 19, 2010 / Details: beryllium lenses
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987872 Å / Relative weight: 1
ReflectionResolution: 1.45→88.05 Å / Num. all: 157910 / Num. obs: 157910 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 17.015
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.503 / % possible all: 98.6

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
ARP/wARPmodel building
CCP4model building
REFMAC5.5.0109refinement
HKL-2000data scaling
DMphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→88.05 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.129 / SU ML: 0.038 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.18 7916 5 %RANDOM
Rwork0.152 ---
obs0.153 157812 99.73 %-
all-157812 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å2-0.04 Å2
2---0.28 Å20 Å2
3---0.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.152 Å
Refinement stepCycle: LAST / Resolution: 1.45→88.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7551 0 10 1205 8766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227745
X-RAY DIFFRACTIONr_bond_other_d0.0010.025119
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.96410511
X-RAY DIFFRACTIONr_angle_other_deg1.009312623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.80551015
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97525.488328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.849151340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5021532
X-RAY DIFFRACTIONr_chiral_restr0.090.21215
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028722
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021430
X-RAY DIFFRACTIONr_mcbond_it0.9521.54980
X-RAY DIFFRACTIONr_mcbond_other0.2561.52052
X-RAY DIFFRACTIONr_mcangle_it1.67628015
X-RAY DIFFRACTIONr_scbond_it2.73232765
X-RAY DIFFRACTIONr_scangle_it4.6424.52487
LS refinement shellResolution: 1.45→1.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 591 -
Rwork0.241 10843 -
obs--98.58 %
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)
10.20150.00030.04290.26610.07560.0324-0.0025-0.00280.00380.0292-0.00310.02940.00710.00580.00560.0206-0.00430.00410.03310.00320.051151.383320.6172-2.2457
20.14980.04780.01290.15850.1770.21680.0135-0.0004-0.00470.006-0.01590.00820.0024-0.0010.00240.030.00180.00260.0437-0.00120.031530.4612-2.505522.9425
30.18990.13940.04880.32790.31120.47860.01620.0165-0.02970.0492-0.015-0.0268-0.0482-0.0275-0.00110.0833-0.009-0.01330.02040.00440.008249.73122.351743.4048
40.1135-0.19620.03630.40390.05020.25650.04290.0128-0.0008-0.0763-0.0470.01220.029-0.00640.00410.04170.0156-0.00140.0303-0.00060.046170.4366-6.6648-19.8971
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 251
2X-RAY DIFFRACTION2B2 - 251
3X-RAY DIFFRACTION3C3 - 250
4X-RAY DIFFRACTION4D2 - 251

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