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- PDB-4gb7: Putative 6-aminohexanoate-dimer hydrolase from Bacillus anthracis -

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Basic information

Entry
Database: PDB / ID: 4gb7
TitlePutative 6-aminohexanoate-dimer hydrolase from Bacillus anthracis
Components6-aminohexanoate-dimer hydrolase
KeywordsHYDROLASE / structural genomics / IDP05595 / 6-aminohexanoate / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


: / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / 6-aminohexanoate-dimer hydrolase / 6-aminohexanoate-dimer hydrolase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsOsipiuk, J. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Putative 6-aminohexanoate-dimer hydrolase from Bacillus anthracis.
Authors: Osipiuk, J. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionJul 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: 6-aminohexanoate-dimer hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4594
Polymers48,2731
Non-polymers1863
Water8,863492
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.696, 61.595, 111.841
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 6-aminohexanoate-dimer hydrolase


Mass: 48273.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BAS3101, BA_3346, GBAA_3346 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81N71, UniProt: A0A6L8PZN3*PLUS
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 0.2 M ammonium nitrate, 20% PEG-3350, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 13, 2012
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→31.8 Å / Num. all: 54699 / Num. obs: 54699 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.114 / Χ2: 2.535 / Net I/σ(I): 14.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.6-1.632.60.4682.0924070.77388.4
1.63-1.663.10.44425790.75692.9
1.66-1.693.90.42226870.78497
1.69-1.724.50.39627880.86999.9
1.72-1.764.90.36227430.98299.9
1.76-1.85.30.31127721.127100
1.8-1.855.70.27127771.305100
1.85-1.96.40.24127701.57499.9
1.9-1.956.50.21527641.83399.9
1.95-2.026.40.17827832.06899.3
2.02-2.096.40.16427552.29699.4
2.09-2.176.40.14627782.55899.6
2.17-2.276.40.13227872.71699
2.27-2.396.30.12127702.87499.2
2.39-2.546.20.11527963.06199.3
2.54-2.746.10.10927823.42499
2.74-3.015.90.10228043.90399
3.01-3.455.60.09327903.95997.2
3.45-4.345.40.0926454.24691.8
4.34-505.50.127226.28489.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→32 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.21 / SU B: 3.143 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.095 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.197 2764 5.1 %RANDOM
Rwork0.1315 ---
all0.1347 54633 --
obs0.1347 54633 97.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.03 Å2 / Biso mean: 24.324 Å2 / Biso min: 13.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2---1.34 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.6→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3092 0 12 492 3596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.023262
X-RAY DIFFRACTIONr_bond_other_d0.0010.022169
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.9524447
X-RAY DIFFRACTIONr_angle_other_deg0.98935343
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3175414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.17225.697165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.14115565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.4341511
X-RAY DIFFRACTIONr_chiral_restr0.1050.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213683
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02624
X-RAY DIFFRACTIONr_rigid_bond_restr4.21535431
X-RAY DIFFRACTIONr_sphericity_free23.9785134
X-RAY DIFFRACTIONr_sphericity_bonded10.24255705
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 172 -
Rwork0.189 3225 -
all-3397 -
obs-3397 88.58 %

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