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- PDB-4k05: Crystal structure of a DUF1343 family protein (BF0371) from Bacte... -

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Basic information

Entry
Database: PDB / ID: 4k05
TitleCrystal structure of a DUF1343 family protein (BF0371) from Bacteroides fragilis NCTC 9343 at 1.65 A resolution
ComponentsConserved hypothetical exported protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF07075 family protein / DUF1343 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


peptidoglycan beta-N-acetylmuramidase activity
Similarity search - Function
Uncharacterised protein PF07075, DUF1343 / Aspartate Aminotransferase, domain 1 - #140 / Exo-beta-N-acetylmuramidase NamZ / : / : / Exo-beta-N-acetylmuramidase NamZ, N-terminal / Exo-beta-N-acetylmuramidase NamZ, C-terminal / Aspartate Aminotransferase, domain 1 / Alpha-Beta Complex / Rossmann fold ...Uncharacterised protein PF07075, DUF1343 / Aspartate Aminotransferase, domain 1 - #140 / Exo-beta-N-acetylmuramidase NamZ / : / : / Exo-beta-N-acetylmuramidase NamZ, N-terminal / Exo-beta-N-acetylmuramidase NamZ, C-terminal / Aspartate Aminotransferase, domain 1 / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / : / Conserved hypothetical exported protein / Conserved hypothetical exported protein
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BF0371) from Bacteroides fragilis NCTC 9343 at 1.65 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: 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 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_atom_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Conserved hypothetical exported protein
B: Conserved hypothetical exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4877
Polymers92,0862
Non-polymers4025
Water21,2941182
1
A: Conserved hypothetical exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0822
Polymers46,0431
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Conserved hypothetical exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4055
Polymers46,0431
Non-polymers3624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-16 kcal/mol
Surface area29800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.080, 88.410, 159.540
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 Conserved hypothetical exported protein


Mass: 46042.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: NCTC 9343 / Gene: BF0371, BF9343_0362 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q5LI85, UniProt: A0A380YTY6*PLUS
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1182 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (27-424) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (27-424) 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: 2.07 Å3/Da / Density % sol: 40.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M potassium formate, 20% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.96109,0.97934
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 5, 2013
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.961091
20.979341
ReflectionResolution: 1.65→29.469 Å / Num. obs: 91531 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.131 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 10.11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.65-1.710.4981.7305621572087.3
1.71-1.780.3792.4381171772097.4
1.78-1.860.2783.3367981705397.4
1.86-1.960.1894.8377781745897
1.96-2.080.1386.4363351678796.6
2.08-2.240.0988.8373751716797.1
2.24-2.460.07910.8366731678996.2
2.46-2.820.06113.6378311723495.7
2.82-3.550.03620.5371161685494.8
3.550.02528.6374031698394.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJuly 4, 2012data scaling
BUSTER-TNTrefinement
XDSdata reduction
SHELXDphasing
autoSHARPphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 1.65→29.469 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.9473 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0
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. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 3. POTASSIUM IONS, FORMATE, PEG ARE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS. 4.NCS RESTRAINTS WERE IMPOSED BY AUTOBUSTER'S LSSR PROCEDURE (-AUTONCS).
RfactorNum. reflection% reflectionSelection details
Rfree0.1826 4574 5 %RANDOM
Rwork0.1491 ---
obs0.1508 91455 98.54 %-
Displacement parametersBiso max: 125.23 Å2 / Biso mean: 19.5263 Å2 / Biso min: 5.72 Å2
Baniso -1Baniso -2Baniso -3
1--1.4392 Å20 Å20 Å2
2---0.4915 Å20 Å2
3---1.9306 Å2
Refine analyzeLuzzati coordinate error obs: 0.149 Å
Refinement stepCycle: LAST / Resolution: 1.65→29.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6189 0 22 1182 7393
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3166SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes159HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1024HARMONIC5
X-RAY DIFFRACTIONt_it6703HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion844SEMIHARMONIC5
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_contact9034SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6703HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9142HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion4.25
X-RAY DIFFRACTIONt_other_torsion2.72
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2376 319 5.44 %
Rwork0.2099 5541 -
all0.2114 5860 -
obs--98.54 %

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