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- PDB-4h4j: Crystal structure of a N-acetylmuramoyl-L-alanine amidase (BACUNI... -

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Basic information

Entry
Database: PDB / ID: 4h4j
TitleCrystal structure of a N-acetylmuramoyl-L-alanine amidase (BACUNI_02947) from Bacteroides uniformis ATCC 8492 at 1.15 A resolution
Componentshypothetical protein
KeywordsStructural Genomics / Unknown Function / PF07313 family protein / DUF 1460 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / STRUCTURAL GENOMICS UNKNOWN FUNCTION
Function / homology
Function and homology information


Putative xylanase fold / Putative xylanase like domain / putative xylanase like fold / putative xylanase like domain / N-acetylmuramoyl-L-alanine amidase-like / N-acetylmuramoyl-L-alanine amidase-like / Papain-like cysteine peptidase superfamily / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DUF1460 domain-containing protein
Similarity search - Component
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.15 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Structure / Year: 2014
Title: Structure-guided functional characterization of DUF1460 reveals a highly specific NlpC/P60 amidase family.
Authors: Xu, Q. / Mengin-Lecreulx, D. / Patin, D. / Grant, J.C. / Chiu, H.J. / Jaroszewski, L. / Knuth, M.W. / Godzik, A. / Lesley, S.A. / Elsliger, M.A. / Deacon, A.M. / Wilson, I.A.
History
DepositionSep 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Sep 18, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein


Theoretical massNumber of molelcules
Total (without water)26,8991
Polymers26,8991
Non-polymers00
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.349, 63.713, 72.962
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 hypothetical protein /


Mass: 26898.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis (bacteria) / Strain: ATCC 8492 / Gene: BACUNI_02947, ZP_02071508.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7V5T8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 431 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (24-262) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (24-262) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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 Å3/Da / Density % sol: 38.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 30.0% polyethylene glycol 1500, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9794
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2012
Details: Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.15→28.666 Å / Num. obs: 71198 / % possible obs: 92.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 11.453 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 12.95
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.15-1.1913.150.8831.8449534870060.2
1.19-1.240.772.4865791330885.7
1.24-1.30.6113.21050671491595.2
1.3-1.360.4224.4828511238695.1
1.36-1.450.3086.21082851511696.5
1.45-1.560.1989974121415997
1.56-1.720.12913.11027251455296.3
1.72-1.970.08219.41002461447597.6
1.97-2.480.05828.81038411454698.9
2.48-28.670.04534.9998451459898.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEMarch 15, 2012data scaling
REFMAC5.5.0110refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.15→28.666 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.972 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 1.11 / SU ML: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.039
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.164 3572 5 %RANDOM
Rwork0.1306 ---
obs0.1323 71147 91.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.69 Å2 / Biso mean: 18.3283 Å2 / Biso min: 5.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.15→28.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1840 0 0 431 2271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222247
X-RAY DIFFRACTIONr_bond_other_d0.0030.021554
X-RAY DIFFRACTIONr_angle_refined_deg1.7561.9823090
X-RAY DIFFRACTIONr_angle_other_deg1.00633889
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.075317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.77325.83396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43415448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.843158
X-RAY DIFFRACTIONr_chiral_restr0.1140.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212547
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02402
X-RAY DIFFRACTIONr_mcbond_it2.74631385
X-RAY DIFFRACTIONr_mcbond_other2.5273551
X-RAY DIFFRACTIONr_mcangle_it3.87152283
X-RAY DIFFRACTIONr_scbond_it4.7218862
X-RAY DIFFRACTIONr_scangle_it6.49611776
X-RAY DIFFRACTIONr_rigid_bond_restr2.23433801
X-RAY DIFFRACTIONr_sphericity_free11.2273452
X-RAY DIFFRACTIONr_sphericity_bonded6.30533727
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 154 -
Rwork0.228 3095 -
all-3249 -
obs--57.23 %

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