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- PDB-3ht4: Crystal Structure of the Q81A77_BACCR Protein from Bacillus cereu... -

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Basic information

Entry
Database: PDB / ID: 3ht4
TitleCrystal Structure of the Q81A77_BACCR Protein from Bacillus cereus. Northeast Structural Genomics Consortium Target BcR213
ComponentsAluminum resistance protein
KeywordsLYASE / putative cystathionine beat-lyase / aluminium resistance protein / Q81A77_BACCR / NESG / BcR213 / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


Putative methionine gamma-lyase / Methionine gamma-lyase / Methioning gamme-lyase, C-terminal domain / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Aluminum resistance protein
Similarity search - Component
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsVorobiev, S. / Lew, S. / Seetharaman, J. / Wang, H. / Foote, E. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Mao, L. / Acton, T.B. ...Vorobiev, S. / Lew, S. / Seetharaman, J. / Wang, H. / Foote, E. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Mao, L. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the Q81A77_BACCR Protein from Bacillus cereus
Authors: Vorobiev, S. / Lew, S. / Seetharaman, J. / Wang, H. / Foote, E. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Mao, L. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJun 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
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 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aluminum resistance protein
B: Aluminum resistance protein
C: Aluminum resistance protein
D: Aluminum resistance protein
E: Aluminum resistance protein
F: Aluminum resistance protein
G: Aluminum resistance protein
H: Aluminum resistance protein


Theoretical massNumber of molelcules
Total (without water)380,4518
Polymers380,4518
Non-polymers00
Water2,270126
1
A: Aluminum resistance protein
B: Aluminum resistance protein
C: Aluminum resistance protein
F: Aluminum resistance protein


Theoretical massNumber of molelcules
Total (without water)190,2264
Polymers190,2264
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15880 Å2
ΔGint-103 kcal/mol
Surface area55000 Å2
MethodPISA
2
D: Aluminum resistance protein
H: Aluminum resistance protein

E: Aluminum resistance protein
G: Aluminum resistance protein


Theoretical massNumber of molelcules
Total (without water)190,2264
Polymers190,2264
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
Buried area15760 Å2
ΔGint-96 kcal/mol
Surface area55040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.406, 144.993, 131.973
Angle α, β, γ (deg.)90.00, 106.24, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTetramer according to aggregation screening

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Components

#1: Protein
Aluminum resistance protein / PUTATIVE CYSTATHIONINE BETA-LYASE


Mass: 47556.414 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Strain: DSM 31 / Gene: BC_3707 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+magic / References: UniProt: Q81A77
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.21 Å3/Da / Density % sol: 44.27 %
Crystal growTemperature: 291 K / Method: microbatch crystallization under parafin oil / pH: 6.15
Details: 20% PEG 3350, 0.15M Malic acid, pH 6.15, Microbatch crystallization under parafin oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97879 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97879 Å / Relative weight: 1
ReflectionResolution: 2.9→500 Å / Num. all: 144584 / Num. obs: 131282 / % possible obs: 90.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.6 % / Biso Wilson estimate: 67.3 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 6.7
Reflection shellResolution: 2.9→3 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 2.2 / Num. unique all: 14504 / % possible all: 91.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FD0, chain A

3fd0


Resolution: 2.9→46.19 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 78329.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.299 5248 4.9 %RANDOM
Rwork0.274 ---
obs0.274 108192 75 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 12.7236 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 30.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å2-2.71 Å2
2--1.91 Å20 Å2
3----0.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.9→46.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24944 0 0 126 25070
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.51
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.317 784 5.1 %
Rwork0.303 14444 -
obs--63.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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