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- PDB-4ghn: Crystal structure of a putative protease (BACUNI_00178) from Bact... -

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Basic information

Entry
Database: PDB / ID: 4ghn
TitleCrystal structure of a putative protease (BACUNI_00178) from Bacteroides uniformis ATCC 8492 at 1.50 A resolution
ComponentsUncharacterized protein
KeywordsHYDROLASE / Putative protease / Peptidase_S41 of PF03572 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


serine-type peptidase activity / proteolysis / membrane
Similarity search - Function
: / Bacteroidetes, Peptidase, S41 family, N-terminal domain / Tricorn protease C1 domain / Tricorn protease C1 domain / Transcription Regulator spoIIAA - #44 / tail specific protease / Tail specific protease / Peptidase family S41 / Transcription Regulator spoIIAA / 2-enoyl-CoA Hydratase; Chain A, domain 1 ...: / Bacteroidetes, Peptidase, S41 family, N-terminal domain / Tricorn protease C1 domain / Tricorn protease C1 domain / Transcription Regulator spoIIAA - #44 / tail specific protease / Tail specific protease / Peptidase family S41 / Transcription Regulator spoIIAA / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / PDZ domain / Pdz3 Domain / ClpP/crotonase-like domain superfamily / PDZ superfamily / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Peptidase, S41 family
Similarity search - Component
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BACUNI_00178) from Bacteroides uniformis ATCC 8492 at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 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 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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
Revision 1.4Nov 6, 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

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8613
Polymers45,6771
Non-polymers1842
Water9,980554
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.077, 102.077, 97.266
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Uncharacterized protein


Mass: 45676.715 Da / Num. of mol.: 1 / Fragment: UNP residues 30-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis (bacteria) / Gene: BACUNI_00178 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7UY07
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 30-421 OF 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: 3.2 Å3/Da / Density % sol: 61.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30.00% Glycerol, 5.60% polyethylene glycol 4000, 0.1M sodium acetate pH 4.6, 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: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2012
Details: Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→17.932 Å / Num. all: 91727 / Num. obs: 91727 / % possible obs: 97.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 15.714 Å2 / Rsym value: 0.112 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.5-1.543.30.5291.42259467680.52998.9
1.54-1.583.10.4361.61966763310.43694.6
1.58-1.633.50.38222228164110.38298.2
1.63-1.683.70.3342.32312463350.33499.7
1.68-1.733.60.2792.72195760910.27999.5
1.73-1.793.60.243.12131158850.2499.3
1.79-1.863.50.1943.82031457340.19499.4
1.86-1.943.40.1634.51841854480.16399
1.94-2.023.40.1444.91638248880.14492
2.02-2.123.90.1335.11957350700.13399.8
2.12-2.243.80.1185.61841348200.11899.4
2.24-2.373.80.11261729645890.11299.8
2.37-2.543.70.1151.31585042930.11599.9
2.54-2.743.40.1026.31302638880.10296.5
2.74-33.50.0996.31205534540.09992.5
3-3.353.90.0976.31299033420.09799.4
3.35-3.873.80.0896.81116329760.08999.6
3.87-4.743.50.087.5874524860.0897.7
4.74-6.713.60.0946.8655318230.09490.9
6.71-17.93240.0818438010950.08194.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.20data scaling
REFMAC5.5.0110refinement
MOSFLMdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→17.932 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.963 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.961 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.055
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. GLYCEROL (GOL) MOLECULES FROM THE CRYSTALLIZATION SOLUTION ARE MODELED. 4. THE SCATTERING FACTORS FOR SULFUR AND SELENIUM ATOMS WERE ADJUSTED BY REFMAC 5.5.0110 TO ACCOUNT FOR ANOMALOUS DISPERSION BASED ON THE WAVELENGTH 0.9795 A (S f'= 0.18, Se f'= -9.64). THE CROMER MANN c VALUES LISTED IN THE CIF VERSION OF THE FILE INCLUDE THIS CORRECTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.1707 4597 5 %RANDOM
Rwork0.1341 ---
obs0.1359 91641 97.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 64.94 Å2 / Biso mean: 21.854 Å2 / Biso min: 8.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.11 Å20 Å2
2--0.23 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.5→17.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3118 0 12 554 3684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223352
X-RAY DIFFRACTIONr_bond_other_d0.0010.022269
X-RAY DIFFRACTIONr_angle_refined_deg1.471.9634581
X-RAY DIFFRACTIONr_angle_other_deg0.9635557
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9315430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99524.593172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.01415574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8021520
X-RAY DIFFRACTIONr_chiral_restr0.1010.2502
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213787
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02688
X-RAY DIFFRACTIONr_mcbond_it2.58732015
X-RAY DIFFRACTIONr_mcbond_other1.7513802
X-RAY DIFFRACTIONr_mcangle_it3.57253298
X-RAY DIFFRACTIONr_scbond_it4.69881337
X-RAY DIFFRACTIONr_scangle_it6.575111263
X-RAY DIFFRACTIONr_rigid_bond_restr1.96935621
X-RAY DIFFRACTIONr_sphericity_free7.8233561
X-RAY DIFFRACTIONr_sphericity_bonded4.53935528
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 322 -
Rwork0.194 6381 -
all-6703 -
obs--98.81 %

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