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- PDB-2etd: Crystal structure of a lema protein (tm0961) from thermotoga mari... -

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Basic information

Entry
Database: PDB / ID: 2etd
TitleCrystal structure of a lema protein (tm0961) from thermotoga maritima msb8 at 2.28 A resolution
ComponentslemA protein
KeywordsMEMBRANE PROTEIN / Bromodomain-like fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyLemA-like domain / MamQ/LemA / LemA-like domain superfamily / LemA family / de novo design (two linked rop proteins) / membrane => GO:0016020 / Up-down Bundle / Mainly Alpha / LemA protein
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.28 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of LEMA protein (tm0961) from THERMOTOGA MARITIMA at 2.28 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Jan 25, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: lemA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9852
Polymers19,9491
Non-polymers351
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.454, 85.259, 53.397
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGIMERIZATION STATE.

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Components

#1: Protein lemA protein


Mass: 19949.291 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: tm0961 / Plasmid: HK100 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X056
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.3
Details: 0.2M NH4NO3, 20.0% PEG-3350, No Buffer pH 6.3 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0163, 0.9797, 0.9796
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 9, 2005
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.01631
20.97971
30.97961
ReflectionResolution: 2.25→30 Å / Num. obs: 8126 / % possible obs: 90.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.067 / Χ2: 1.03
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. measured obsΧ2Diffraction-ID
2.25-2.33623.50.3325491.081
2.33-2.4299.93.60.1778721.0431
2.42-2.5399.33.60.1588871.061
2.53-2.6799.83.60.1448941.0661
2.67-2.8399.33.60.1128761.0021
2.83-3.0599.23.60.0888890.9961
3.05-3.3698.53.60.0778761.0171
3.36-3.8564.93.30.0785870.9941
3.85-4.8484.53.50.0547791.0391
4.84-3094.33.40.0419171.0121

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PDB_EXTRACT1.601data extraction
DENZOdata reduction
HKL-2000data scaling
SHELXphasing
SHARPphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MAD / Resolution: 2.28→26.7 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.913 / SU B: 13.938 / SU ML: 0.175 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.318 / ESU R Free: 0.25
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 0.7 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. THE STRUCTURE WAS NOT MODELED BETWEEN 162-171 BECAUSE THE ELECTRON DENSITY IN THIS REGION IS DISORDERED. 4. THIS PROTEIN IS REDUCTIVELY METHYLATED. HOWEVER, DENSITY FOR MOST OF THE METHYL GROUPS ARE NOT OBSERVED, MAYBE DUE TO FLEXIBILITY OR LIMITED RESOLUTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 375 4.6 %RANDOM
Rwork0.216 ---
all0.219 ---
obs-7717 93.03 %-
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 mean: 40.488 Å2
Baniso -1Baniso -2Baniso -3
1--1.66 Å20 Å20 Å2
2--1.78 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.28→26.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 0 1 62 1169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221119
X-RAY DIFFRACTIONr_bond_other_d0.0010.021023
X-RAY DIFFRACTIONr_angle_refined_deg1.3621.9681505
X-RAY DIFFRACTIONr_angle_other_deg0.83532384
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.255139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.77325.26357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04915208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.674158
X-RAY DIFFRACTIONr_chiral_restr0.0760.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021246
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02210
X-RAY DIFFRACTIONr_nbd_refined0.2180.2259
X-RAY DIFFRACTIONr_nbd_other0.1680.2927
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2540
X-RAY DIFFRACTIONr_nbtor_other0.0850.2656
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.241
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3860.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.26
X-RAY DIFFRACTIONr_mcbond_it2.2433735
X-RAY DIFFRACTIONr_mcbond_other0.5623284
X-RAY DIFFRACTIONr_mcangle_it3.35451116
X-RAY DIFFRACTIONr_scbond_it5.9658449
X-RAY DIFFRACTIONr_scangle_it8.61711389
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 22 -
Rwork0.24 568 -
obs--93.21 %
Refinement TLS params.Method: refined / Origin x: 14.1683 Å / Origin y: 28.8656 Å / Origin z: 53.6444 Å
111213212223313233
T-0.1623 Å2-0.0042 Å2-0.0423 Å2--0.2821 Å20.0024 Å2---0.124 Å2
L3.4018 °20.1682 °2-2.1498 °2-1.0196 °2-0.8106 °2--6.6168 °2
S0.0338 Å °-0.0457 Å °0.2954 Å °0.0509 Å °0.0258 Å °-0.0354 Å °-0.3101 Å °0.1317 Å °-0.0596 Å °

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