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- PDB-4r4k: Crystal structure of a cystatin-like protein (BACCAC_01506) from ... -

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Basic information

Entry
Database: PDB / ID: 4r4k
TitleCrystal structure of a cystatin-like protein (BACCAC_01506) from Bacteroides caccae ATCC 43185 at 1.69 A resolution
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Cystatin-like fold / divergent member of PF14254 family (DUF4348) / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyNuclear Transport Factor 2; Chain: A, - #410 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / ACETATE ION / Uncharacterized protein
Function and homology information
Biological speciesBacteroides caccae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.69 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BACCAC_01506) from Bacteroides caccae ATCC 43185 at 1.69 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 22, 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 / 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 1.5Oct 9, 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: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,05727
Polymers71,5034
Non-polymers16,55423
Water11,205622
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7538
Polymers17,8761
Non-polymers3,8777
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7246
Polymers17,8761
Non-polymers3,8495
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0187
Polymers17,8761
Non-polymers6,1436
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5626
Polymers17,8761
Non-polymers2,6865
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.355, 62.823, 115.349
Angle α, β, γ (deg.)90.000, 106.570, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Uncharacterized protein


Mass: 17875.715 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides caccae (bacteria) / Strain: ATCC 43185 / Gene: BACCAC_01506 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A5ZF42

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Non-polymers , 5 types, 645 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-PEU / 2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56,59,62,65,68,71,74,77,80-HEPTACOSAOXADOOCTACONTAN-82-OL / PEG 8000


Mass: 1221.461 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C55H112O28 / Comment: precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 622 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 33-185 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: 2.61 Å3/Da / Density % sol: 52.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 26.0% polyethylene glycol 8000, 0.2M lithium sulfate, 0.1M sodium acetate pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97946
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 14, 2014 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979461
ReflectionResolution: 1.69→29.757 Å / Num. obs: 81133 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.881 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 6.96
Reflection shell

Rmerge(I) obs: 0.015 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Mean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.7-1.761451521552498.4
1.76-1.831.4472951578199.2
1.83-1.912453121517398.5
1.91-2.023515711721298.6
2.02-2.144.4446531488698.5
2.14-2.315.8489321625298.6
2.31-2.547.3469661557099.3
2.54-2.910.1470421558199.3
2.9-3.6614.9478961604398.7
3.6619.5462511568398.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
REFMAC5.7.0032refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.69→29.757 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 4.208 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.098
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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. POLYETHYLENE GLYCOL (PEU), SULFATE (SO4) AND GLYCEROL (GOL) FROM THE CRYOPROTECTANT AND FROM THE CRYSTALLIZATION CONDITION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 4. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 5. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2026 4046 5 %RANDOM
Rwork0.1752 ---
obs0.1765 80945 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 116.68 Å2 / Biso mean: 29.6425 Å2 / Biso min: 11.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20.27 Å2
2---0.13 Å2-0 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.69→29.757 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4916 0 199 622 5737
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.025488
X-RAY DIFFRACTIONr_bond_other_d0.0070.025061
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.9847409
X-RAY DIFFRACTIONr_angle_other_deg1.348311838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2195674
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.40125.739284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.06615934
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4451514
X-RAY DIFFRACTIONr_chiral_restr0.0870.2760
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216124
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021194
X-RAY DIFFRACTIONr_mcbond_it2.6674.0452503
X-RAY DIFFRACTIONr_mcbond_other2.6584.0332498
X-RAY DIFFRACTIONr_mcangle_it3.9217.5443142
LS refinement shellResolution: 1.695→1.739 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 262 -
Rwork0.3 5286 -
all-5548 -
obs--92.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2660.0587-0.29360.2970.0490.4779-0.02080.00160.0136-0.04670.0269-0.0262-0.0158-0.0597-0.00610.03840.0263-0.01340.0543-0.02210.013212.473610.97828.4868
20.395-0.0291-0.24790.8077-0.02530.16280.0355-0.04210.03840.0007-0.01990.0263-0.00990.026-0.01550.0311-0.0082-0.00290.0205-0.00760.04329.900635.23931.6767
30.201-0.07130.06880.3219-0.00250.2420.0481-0.0039-0.0306-0.0236-0.0579-0.0168-0.0079-0.00120.00970.02580.0129-0.00920.02680.0050.044230.7128-1.104428.7857
40.40340.05580.05320.05090.15970.57160.0125-0.0186-0.0198-0.0068-0.0104-0.0106-0.0364-0.0498-0.0020.00820.0119-0.0050.0416-0.02190.03672.818622.563141.008
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 185
2X-RAY DIFFRACTION2B34 - 185
3X-RAY DIFFRACTION3C35 - 185
4X-RAY DIFFRACTION4D38 - 185

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