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- PDB-3io1: Crystal Structure of Aminobenzoyl-glutamate utilization protein f... -

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Basic information

Entry
Database: PDB / ID: 3io1
TitleCrystal Structure of Aminobenzoyl-glutamate utilization protein from Klebsiella pneumoniae
ComponentsAminobenzoyl-glutamate utilization protein
KeywordsHYDROLASE / Aminobenzoyl-glutamate utilization protein / Peptidase_M20D superfamily / Protein Structure Initiative II / NYSGXRC / 11203b / Structural Genomics / PSI-2 / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
Similarity search - Function
p-Aminobenzoyl-glutamate hydrolase subunit A / Amidohydrolase / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase ...p-Aminobenzoyl-glutamate hydrolase subunit A / Amidohydrolase / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
YTTRIUM (III) ION / Aminobenzoyl-glutamate utilization protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsKumaran, D. / Baumann, K. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Aminobenzoyl-glutamate utilization protein from Klebsiella pneumoniae
Authors: Kumaran, D. / Baumann, K. / Burley, S.K. / Swaminathan, S.
History
DepositionAug 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Aminobenzoyl-glutamate utilization protein
B: Aminobenzoyl-glutamate utilization protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1915
Polymers97,0562
Non-polymers1353
Water1,69394
1
A: Aminobenzoyl-glutamate utilization protein
B: Aminobenzoyl-glutamate utilization protein
hetero molecules

A: Aminobenzoyl-glutamate utilization protein
B: Aminobenzoyl-glutamate utilization protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,38110
Polymers194,1124
Non-polymers2706
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area10670 Å2
ΔGint-96 kcal/mol
Surface area59800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.390, 48.519, 107.998
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Aminobenzoyl-glutamate utilization protein


Mass: 48527.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria)
Strain: strain ATCC 700721 / MGH 78578 / Gene: abgA, KPN78578_15040, KPN_01534 / Plasmid: pSGX3(BC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A6T8P4
#2: Chemical ChemComp-YT3 / YTTRIUM (III) ION


Mass: 88.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Y
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.48 Å3/Da / Density % sol: 50.31 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Malic acid, 20% PEG 3350, 0.01 M Yttrium Chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2009 / Details: mirrors
RadiationMonochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 34494 / Num. obs: 34494 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 13.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1 / Num. unique all: 3350 / % possible all: 97.7

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXDphasing
SHARPphasing
ARP/wARPmodel building
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→43.02 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 71876.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1667 5 %RANDOM
Rwork0.224 ---
obs0.224 33359 97.2 %-
all-33359 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.0503 Å2 / ksol: 0.342959 e/Å3
Displacement parametersBiso mean: 43.1 Å2
Baniso -1Baniso -2Baniso -3
1--4.68 Å20 Å20 Å2
2--12.07 Å20 Å2
3----7.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.5→43.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5898 0 3 94 5995
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.81
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.303 265 5.1 %
Rwork0.268 4886 -
obs--92 %

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