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- PDB-3p8k: Crystal Structure of a putative carbon-nitrogen family hydrolase ... -

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Basic information

Entry
Database: PDB / ID: 3p8k
TitleCrystal Structure of a putative carbon-nitrogen family hydrolase from Staphylococcus aureus
ComponentsHydrolase, carbon-nitrogen family
KeywordsHYDROLASE
Function / homology
Function and homology information


: / hydrolase activity
Similarity search - Function
Uncharacterised protein family UPF0012, conserved site / Uncharacterized protein family UPF0012 signature. / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Hydrolase, carbon-nitrogen family / Hydrolase, carbon-nitrogen family
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus COL (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsGordon, R.D. / Qiu, W. / Battaile, K. / Lam, K. / Soloveychik, M. / Benetteraj, D. / Romanov, V. / Pai, E.F. / Chirgadze, N.Y.
CitationJournal: To be Published
Title: Crystal Structure of carbon-nitrogen family hydrolase from Staphylococcus aureus
Authors: Qiu, W. / Gordon, R.D. / Battaile, K. / Lam, K. / Soloveychik, M. / Benetteraj, D. / Romanov, V. / Pai, E.F. / Chirgadze, N.Y.
History
DepositionOct 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 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

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Assembly

Deposited unit
A: Hydrolase, carbon-nitrogen family
B: Hydrolase, carbon-nitrogen family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,68313
Polymers64,7082
Non-polymers97511
Water9,998555
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-38 kcal/mol
Surface area21140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.580, 61.980, 155.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE BIOLOGICAL ASSEMBLY IS UNKNOWN AS PER AUTHORS

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Hydrolase, carbon-nitrogen family / carbon-nitrogen family hydrolase


Mass: 32354.229 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus COL (bacteria)
Strain: COL / Gene: SACOL2021 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5HEG7, UniProt: A0A0H2WXM0*PLUS

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Non-polymers , 6 types, 566 molecules

#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.18 Å3/Da / Density % sol: 43.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.2
Details: 0.2M magnesium chloride, 0.1M TRIS, pH 8.2, 25% PEG 3350, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 3, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 62691 / Num. obs: 61246 / % possible obs: 97.9 % / Redundancy: 25 % / Biso Wilson estimate: 20.07 Å2 / Rsym value: 0.0803 / Net I/σ(I): 18.1
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.83 / Num. unique all: 7994 / Rsym value: 0.458 / % possible all: 85.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
BUSTER2.8.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→19.96 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.9197 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2302 3060 5.06 %RANDOM
Rwork0.1974 ---
obs0.199 60527 --
Displacement parametersBiso mean: 23.55 Å2
Baniso -1Baniso -2Baniso -3
1--3.3647 Å20 Å20 Å2
2---2.6628 Å20 Å2
3---6.0275 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4318 0 59 555 4932
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0145002
X-RAY DIFFRACTIONt_angle_deg1.1460982
X-RAY DIFFRACTIONt_dihedral_angle_d15822
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes1472
X-RAY DIFFRACTIONt_gen_planes6365
X-RAY DIFFRACTIONt_it450020
X-RAY DIFFRACTIONt_nbd45
X-RAY DIFFRACTIONt_omega_torsion3.74
X-RAY DIFFRACTIONt_other_torsion17.47
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion5665
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact56844
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2529 170 5.39 %
Rwork0.2362 2983 -
all0.237 3153 -

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