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- PDB-4qrk: Crystal structure of a putative cell adhesion protein (CLOSPO_037... -

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Basic information

Entry
Database: PDB / ID: 4qrk
TitleCrystal structure of a putative cell adhesion protein (CLOSPO_03726) from Clostridium sporogenes ATCC 15579 at 1.95 A resolution
ComponentsHypothetical protein
KeywordsCELL ADHESION / Right-handed beta-helix / PF09922 family / DUF2154 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyCell wall-active antibiotics response 4TMS YvqF / Uncharacterised protein DUF2154, N-terminal / Cell wall-active antibiotics response LiaF, C-terminal / N-terminal domain of toast_rack, DUF2154 / metal ion binding / ACETATE ION / Uncharacterized protein
Function and homology information
Biological speciesClostridium sporogenes ATCC 15579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (CLOSPO_03726) from Clostridium sporogenes ATCC 15579 at 1.95 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2063
Polymers24,1071
Non-polymers992
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.348, 72.348, 109.470
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Hypothetical protein /


Mass: 24107.018 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium sporogenes ATCC 15579 (bacteria)
Gene: CLOSPO_03726, ZP_02996603.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: J7TBR0
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 29-247 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: 3.43 Å3/Da / Density % sol: 64.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.16M calcium acetate, 20.0% Glycerol, 14.4000% polyethylene glycol 8000, 0.1M sodium cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.95369,0.97939,0.97920
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 8, 2014
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
10.953691
20.979391
30.97921
ReflectionResolution: 1.95→62.656 Å / Num. all: 23708 / Num. obs: 23708 / % possible obs: 100 % / Redundancy: 4.7 % / Rsym value: 0.1 / Net I/σ(I): 7.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.95-24.70.820.9818417400.82100
2-2.064.70.6551.1807717160.655100
2.06-2.124.70.5521.3779916440.552100
2.12-2.184.70.4091.8753015950.409100
2.18-2.254.70.3072.4743615790.307100
2.25-2.334.80.2672.8718115100.267100
2.33-2.424.70.2483693414640.248100
2.42-2.524.80.233.3657813840.23100
2.52-2.634.80.2063.7638213410.206100
2.63-2.764.80.1734.3610912860.173100
2.76-2.914.80.1265.9587612330.126100
2.91-3.084.80.1116.6549811520.111100
3.08-3.34.80.0916.9526911070.091100
3.3-3.564.80.0827.4479010030.082100
3.56-3.94.80.0638.444269280.063100
3.9-4.364.80.05111.241058600.051100
4.36-5.044.70.04111.835707560.041100
5.04-6.174.70.0471329586250.047100
6.17-8.724.70.05810.123545030.058100
8.72-62.6564.50.0628.312602820.06299.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SOLVEphasing
SCALA3.3.20data scaling
PHENIX1.8.2refinement
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.95→62.656 Å / Occupancy max: 1 / Occupancy min: 0.37 / SU ML: 0.18 / σ(F): 1.42 / Phase error: 19.75 / Stereochemistry target values: MLHL
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. CALCIUM (CA) AND ACETATE (ACT) IONS FROM THE CRYSTALLIZATION SOLUTION ARE MODELED.
RfactorNum. reflection% reflection
Rfree0.2064 1216 5.15 %
Rwork0.1647 --
obs0.1668 23634 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.85 Å2 / Biso mean: 39.8944 Å2 / Biso min: 16.45 Å2
Refinement stepCycle: LAST / Resolution: 1.95→62.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1628 0 5 158 1791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141699
X-RAY DIFFRACTIONf_angle_d1.5482292
X-RAY DIFFRACTIONf_chiral_restr0.09255
X-RAY DIFFRACTIONf_plane_restr0.006301
X-RAY DIFFRACTIONf_dihedral_angle_d15.357674
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9501-2.02820.25341210.236824782599
2.0282-2.12050.2471410.220524902631
2.1205-2.23230.26631250.189424822607
2.2323-2.37210.19451340.169724882622
2.3721-2.55520.24561410.172124842625
2.5552-2.81230.23731610.167524562617
2.8123-3.21910.18991370.162624912628
3.2191-4.05520.18021420.13725092651
4.0552-41.23040.18481140.155925402654
Refinement TLS params.Method: refined / Origin x: 20.2128 Å / Origin y: 12.9512 Å / Origin z: 15.7039 Å
111213212223313233
T0.1918 Å20.0186 Å2-0.0089 Å2-0.1956 Å2-0.0077 Å2--0.2069 Å2
L0.6927 °20.1065 °2-0.181 °2-0.3396 °20.2609 °2--0.9788 °2
S-0.0042 Å °-0.0116 Å °-0.0045 Å °0.0106 Å °0.0288 Å °-0.0828 Å °-0.055 Å °-0.0272 Å °-0 Å °
Refinement TLS groupSelection details: (chain A and resseq 36:247)

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