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- PDB-3n73: Crystal structure of a putative 4-hydroxy-2-oxoglutarate aldolase... -

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Basic information

Entry
Database: PDB / ID: 3n73
TitleCrystal structure of a putative 4-hydroxy-2-oxoglutarate aldolase from Bacillus cereus
ComponentsPutative 4-hydroxy-2-oxoglutarate aldolase
KeywordsLYASE / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology2-dehydro-3-deoxy-phosphogluconate aldolase / KDGP aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / 2-dehydro-3-deoxyphosphooctonate aldolase
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.07 Å
AuthorsCabello, R. / Chruszcz, M. / Xu, X. / Zimmerman, M.D. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of a putative 4-hydroxy-2-oxoglutarate aldolase from Bacillus cereus
Authors: Cabello, R. / Chruszcz, M. / Xu, X. / Zimmerman, M.D. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W.
History
DepositionMay 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 27, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative 4-hydroxy-2-oxoglutarate aldolase
B: Putative 4-hydroxy-2-oxoglutarate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4795
Polymers54,3732
Non-polymers1063
Water5,891327
1
A: Putative 4-hydroxy-2-oxoglutarate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2573
Polymers27,1861
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative 4-hydroxy-2-oxoglutarate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2222
Polymers27,1861
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.066, 166.644, 37.279
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

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Components

#1: Protein Putative 4-hydroxy-2-oxoglutarate aldolase


Mass: 27186.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 10987 / Gene: BCE_5001 / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) (Stratagene) / References: UniProt: Q72YM0
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.32 Å3/Da / Density % sol: 46.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6.5
Details: 0.1M BIS-TRIS PH6.5, 0.2M NACL, 25% PEG3350, VAPOR DIFFUSION - HANGING DROP, TEMPERATURE 273K, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2008 / Details: MIRROR
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 30820 / Num. obs: 30820 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / Net I/σ(I): 26.371
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.673 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1452 / Rsym value: 0.673 / % possible all: 66.6

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
ARP/wARPmodel building
REFMAC5.5.0109refinement
Cootmodel building
HKL-3000data reduction
HKL-2000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.07→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.059 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.204 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22128 1561 5.1 %RANDOM
Rwork0.16892 ---
all0.17161 29151 --
obs0.17161 29151 96.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.068 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2--0.48 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.07→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3775 0 3 327 4105
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223835
X-RAY DIFFRACTIONr_bond_other_d0.0080.022548
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.9635195
X-RAY DIFFRACTIONr_angle_other_deg0.93236265
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1455497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.71825.185162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.69215658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4091518
X-RAY DIFFRACTIONr_chiral_restr0.0840.2599
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214307
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02717
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6591.52467
X-RAY DIFFRACTIONr_mcbond_other0.1961.51022
X-RAY DIFFRACTIONr_mcangle_it1.15923963
X-RAY DIFFRACTIONr_scbond_it2.09331368
X-RAY DIFFRACTIONr_scangle_it3.4794.51232
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3158 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.30.5
medium thermal0.582
LS refinement shellResolution: 2.071→2.125 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 86 -
Rwork0.218 1436 -
obs--66.58 %
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)
12.52920.1347-2.31531.80880.51216.4263-0.1674-0.0280.1537-0.1165-0.00090.2037-0.2122-0.33030.16830.08350.04-0.08410.058-0.01440.108659.22958.258-12.737
23.5572-0.64950.61026.2939-1.61954.4714-0.1685-0.3449-0.07210.41170.17880.3754-0.0067-0.3587-0.01020.07370.04960.0290.1294-0.04540.101952.97347.058-4.17
30.86710.03230.18841.18740.36850.6865-0.0579-0.08550.01010.03230.0525-0.0432-0.03330.00210.00540.04340.0234-0.01450.05690.00790.031869.71744.64-12.094
46.6239-0.4003-8.93844.5568-1.130117.40220.0824-0.26680.5074-0.16960.0082-0.2424-0.70120.2063-0.09060.13640.0012-0.06690.0401-0.01630.163269.42165.625-13.783
52.4421-0.0631-1.08242.45330.81964.2796-0.143-0.04190.2636-0.24040.01070.2918-0.4102-0.31840.13220.19320.0151-0.10990.0385-0.00650.190515.28379.93119.321
61.81150.0418-1.5694.4166-0.0652.1457-0.1448-0.30360.18330.19030.14130.11990.0321-0.05580.00350.13230.0492-0.01740.2004-0.06050.149611.12367.21627.98
70.70320.07450.04292.01190.25490.8634-0.0778-0.02930.0982-0.13380.0625-0.119-0.17750.07060.01530.0964-0.0414-0.00860.05650.00630.074828.26266.06218.387
82.59370.2321-0.0972.2526-0.50915.6923-0.1212-0.29170.32010.03060.01790.0698-0.5263-0.12730.10330.1477-0.0074-0.08140.0638-0.03890.161723.10283.45924.191
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 39
2X-RAY DIFFRACTION2A40 - 74
3X-RAY DIFFRACTION3A75 - 233
4X-RAY DIFFRACTION4A234 - 250
5X-RAY DIFFRACTION5B2 - 39
6X-RAY DIFFRACTION6B40 - 76
7X-RAY DIFFRACTION7B77 - 213
8X-RAY DIFFRACTION8B214 - 250

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