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- PDB-3c8l: Crystal structure of a ftsz-like protein of unknown function (npu... -

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Basic information

Entry
Database: PDB / ID: 3c8l
TitleCrystal structure of a ftsz-like protein of unknown function (npun_r1471) from nostoc punctiforme pcc 73102 at 1.22 A resolution
ComponentsFtsZ-like protein of unknown function
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyTubulin/FtsZ, C-terminal domain / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta / IMIDAZOLE
Function and homology information
Biological speciesNostoc punctiforme (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.22 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of FtsZ-like protein of unknown function (ZP_00109722.1) from Nostoc punctiforme PCC 73102 at 1.22 A resolution.
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_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 30, 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: FtsZ-like protein of unknown function
B: FtsZ-like protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,85712
Polymers27,0792
Non-polymers77810
Water4,378243
1
A: FtsZ-like protein of unknown function
B: FtsZ-like protein of unknown function
hetero molecules

A: FtsZ-like protein of unknown function
B: FtsZ-like protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,71424
Polymers54,1594
Non-polymers1,55520
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area9270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.418, 78.628, 75.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-186-

HOH

21B-176-

HOH

31B-230-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein FtsZ-like protein of unknown function


Mass: 13539.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme (bacteria) / Strain: PCC 73102 / Gene: ZP_00109722.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100

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Non-polymers , 5 types, 253 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence details1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED ...1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE. 2. THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. THE SEQUENCE INFORMATION IS AVAILABLE AT GENBANK WITH ACCESSION CODE ZP_00109722.1 AND FROM THE UNIPROT ARCHIVE (UNIPARC) WITH ACCESSION CODE UPI000038D0CC.

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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: 2.05 Å3/Da / Density % sol: 40.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: NANODROP, 2.0M (NH4)2SO4, 0.1M Tris-HCl pH 8.5, 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, 0.97978, 0.97964
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 12, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979781
30.979641
ReflectionResolution: 1.22→44.065 Å / Num. obs: 65528 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 10.538 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 11.5
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.22-1.260.5181.8116865785195.5
1.26-1.310.4722.5201506525199
1.31-1.370.4043.2236986652199.7
1.37-1.450.324.1260447283199.7
1.45-1.540.2215.8232856457199.4
1.54-1.660.1478.3238466596199.4
1.66-1.820.111.6228236289199
1.82-2.090.06416.8251646705198.3
2.09-2.630.05425.8394126568199
2.63-44.0650.03834.4471336668196.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.22→44.065 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.418 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.044
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. CHLORIDE, SULFATE, IMIDAZOLE AND GLYCEROL WERE MODELED BASED ON PURIFICATION, CRYSTALLIZATION AND CRYOPROTECTION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.184 3334 5.1 %RANDOM
Rwork0.158 ---
obs0.159 65514 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.411 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2---0.25 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.22→44.065 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1783 0 44 243 2070
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222072
X-RAY DIFFRACTIONr_bond_other_d0.0030.021351
X-RAY DIFFRACTIONr_angle_refined_deg1.7461.9852864
X-RAY DIFFRACTIONr_angle_other_deg1.08533368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6515300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.54825.06379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.54415362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.551513
X-RAY DIFFRACTIONr_chiral_restr0.110.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022364
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02374
X-RAY DIFFRACTIONr_nbd_refined0.2070.3365
X-RAY DIFFRACTIONr_nbd_other0.1960.31489
X-RAY DIFFRACTIONr_nbtor_refined0.1610.51002
X-RAY DIFFRACTIONr_nbtor_other0.0860.51071
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.5278
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.322
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2320.351
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.557
X-RAY DIFFRACTIONr_mcbond_it1.72521392
X-RAY DIFFRACTIONr_mcbond_other0.7642529
X-RAY DIFFRACTIONr_mcangle_it2.25332185
X-RAY DIFFRACTIONr_scbond_it2.1072777
X-RAY DIFFRACTIONr_scangle_it2.9523658
X-RAY DIFFRACTIONr_rigid_bond_restr1.2233672
X-RAY DIFFRACTIONr_sphericity_free6.2413246
X-RAY DIFFRACTIONr_sphericity_bonded2.98233370
LS refinement shellResolution: 1.22→1.252 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 246 -
Rwork0.267 4376 -
all-4622 -
obs--95.2 %

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