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- PDB-4fd0: Crystal structure of a putative cell surface protein (BACCAC_0370... -

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Basic information

Entry
Database: PDB / ID: 4fd0
TitleCrystal structure of a putative cell surface protein (BACCAC_03700) from Bacteroides caccae ATCC 43185 at 2.07 A resolution
ComponentsLeucine rich hypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / putative cell surface protein / Big3 domain / LRR domain / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


Immunoglobulin-like - #3630 / Bacterial Ig-like domain (group 3) / Ig-like domain, bacterial type / BspA type Leucine rich repeat region / BspA type Leucine rich repeat region (6 copies) / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat domain superfamily / Immunoglobulin-like ...Immunoglobulin-like - #3630 / Bacterial Ig-like domain (group 3) / Ig-like domain, bacterial type / BspA type Leucine rich repeat region / BspA type Leucine rich repeat region (6 copies) / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Bacterial group 3 Ig-like protein
Similarity search - Component
Biological speciesBacteroides caccae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.07 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a leucine rich hypothetical protein (BACCAC_03700) from Bacteroides caccae ATCC 43185 at 2.07 A resolution (CASP Target)
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
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: Leucine rich hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,28318
Polymers44,7101
Non-polymers1,57217
Water8,287460
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.241, 104.103, 153.954
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Leucine rich hypothetical protein


Mass: 44710.203 Da / Num. of mol.: 1 / Fragment: UNP residues 26-428
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides caccae (bacteria) / Gene: BACCAC_03700 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: A5ZLA0
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 26-428) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 26-428) 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: 3.91 Å3/Da / Density % sol: 68.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 0.200M lithium sulfate, 2.00M ammonium sulfate, 0.1M CAPS pH 10.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97932,0.91837,0.97862
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2012
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979321
20.918371
30.978621
ReflectionResolution: 2.07→46.029 Å / Num. obs: 42010 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 32.803 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 12.27
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.07-2.140.8181.8139964054199.3
2.14-2.230.6252.4150974418198.8
2.23-2.330.4443.1139334154199
2.33-2.450.3353.8127943999195.9
2.45-2.610.2415.4152784389198.8
2.61-2.810.1787144814172198.4
2.81-3.090.111.5140284179197.8
3.09-3.530.05220.4138844094196
3.53-4.440.03130.5140164221196.7
4.44-46.0290.02636.3141994274193.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 29, 2011data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.07→46.029 Å / Cor.coef. Fo:Fc: 0.9434 / Cor.coef. Fo:Fc free: 0.9319 / 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. CHLORIDE, SULFATE MODELED WERE PRESENT IN THE PROTEIN/CRYSTALLIZATION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2049 2118 5.04 %RANDOM
Rwork0.1766 ---
obs0.1781 42003 97.5 %-
Displacement parametersBiso max: 100.83 Å2 / Biso mean: 37.2084 Å2 / Biso min: 19.22 Å2
Baniso -1Baniso -2Baniso -3
1-2.2984 Å20 Å20 Å2
2---11.3676 Å20 Å2
3---9.0692 Å2
Refine analyzeLuzzati coordinate error obs: 0.231 Å
Refinement stepCycle: LAST / Resolution: 2.07→46.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3032 0 81 460 3573
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1490SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes86HARMONIC2
X-RAY DIFFRACTIONt_gen_planes455HARMONIC5
X-RAY DIFFRACTIONt_it3213HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion439SEMIHARMONIC5
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_contact3946SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3213HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4388HARMONIC21.14
X-RAY DIFFRACTIONt_omega_torsion3.9
X-RAY DIFFRACTIONt_other_torsion2.58
LS refinement shellResolution: 2.07→2.12 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2406 139 4.42 %
Rwork0.2228 3006 -
all0.2236 3145 -
obs--97.5 %

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