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- PDB-4dcz: Crystal structure of a domain from a mycoplasma genitalium termin... -

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Basic information

Entry
Database: PDB / ID: 4dcz
TitleCrystal structure of a domain from a mycoplasma genitalium terminal organelle protein
ComponentsDnaJ-like protein MG200
KeywordsUNKNOWN FUNCTION / DIMER / INTRA-DOMAIN SYMMETRY AXIS
Function / homology
Function and homology information


chaperone cofactor-dependent protein refolding / unfolded protein binding / protein refolding / cytoplasm
Similarity search - Function
Alpha-Beta Plaits - #3600 / Enriched in aromatic and glycine residues box / EAGR domain superfamily / Enriched in aromatic and glycine Residues box / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain ...Alpha-Beta Plaits - #3600 / Enriched in aromatic and glycine residues box / EAGR domain superfamily / Enriched in aromatic and glycine Residues box / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DnaJ-like protein MG200
Similarity search - Component
Biological speciesMycoplasma genitalium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsCalisto, B.M. / Martinelli, L. / Fita, I.
CitationJournal: Mol.Microbiol. / Year: 2012
Title: The EAGR box structure: a motif involved in mycoplasma motility.
Authors: Calisto, B.M. / Broto, A. / Martinelli, L. / Querol, E. / Pinol, J. / Fita, I.
History
DepositionJan 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DnaJ-like protein MG200
B: DnaJ-like protein MG200


Theoretical massNumber of molelcules
Total (without water)21,8772
Polymers21,8772
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DnaJ-like protein MG200


Theoretical massNumber of molelcules
Total (without water)10,9391
Polymers10,9391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: DnaJ-like protein MG200


Theoretical massNumber of molelcules
Total (without water)10,9391
Polymers10,9391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.003, 81.003, 73.297
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsBIOMOLECULE: 1, 2, 3 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. BIOMOLECULE: 1 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC APPLY THE FOLLOWING TO CHAINS: A, B BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 BIOMOLECULE: 2 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC SOFTWARE USED: PISA APPLY THE FOLLOWING TO CHAINS: B BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 BIOMOLECULE: 3 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC SOFTWARE USED: PISA APPLY THE FOLLOWING TO CHAINS: A BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000

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Components

#1: Protein DnaJ-like protein MG200


Mass: 10938.724 Da / Num. of mol.: 2 / Fragment: TO PROTEIN DOMAIN (UNP RESIDUES 124-207)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma genitalium (bacteria) / Strain: G37 / Gene: MG200 / Plasmid: PET21D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P47442

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 22% PEG 2000, 0.1 M SODIUM CITRATE, PH 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONESRF ID14-410.9790.979
SYNCHROTRONESRF ID14-420.979
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 315r1CCDJul 26, 2009MIRRORS
ADSC QUANTUM 315r2CCDNov 1, 2009MIRRORS
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI 111 CHANNELSINGLE WAVELENGTHMx-ray1
2SI 111 CHANNELSADMx-ray1
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 6450 / % possible obs: 74 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Biso Wilson estimate: 70 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.066 / Net I/σ(I): 32.7
Reflection shellResolution: 2.9→3 Å / Redundancy: 10 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 5.2 / Rsym value: 0.393 / % possible all: 90

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Processing

Software
NameVersionClassification
SHELXDphasing
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.9→27.18 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.882 / SU B: 25.518 / SU ML: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.26 294 4.6 %RANDOM
Rwork0.203 ---
obs0.206 6418 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.9→27.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms922 0 0 0 922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021954
X-RAY DIFFRACTIONr_bond_other_d0.0010.02640
X-RAY DIFFRACTIONr_angle_refined_deg1.7051.891298
X-RAY DIFFRACTIONr_angle_other_deg0.93531536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5715108
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46125.17258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.30215142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg31.237154
X-RAY DIFFRACTIONr_chiral_restr0.0910.2116
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021092
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02214
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7061.5540
X-RAY DIFFRACTIONr_mcbond_other0.1311.5226
X-RAY DIFFRACTIONr_mcangle_it1.3562860
X-RAY DIFFRACTIONr_scbond_it1.9023414
X-RAY DIFFRACTIONr_scangle_it3.0864.5438
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 15 -
Rwork0.333 425 -
obs--96.49 %
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)
10.19752.16382.473128.299432.984538.52540.25750.0843-0.0031-0.1163-0.71980.1759-0.2917-1.23910.46230.77470.1163-0.04391.18460.19970.912214.826160.889349.6763
25.2715-2.7881-0.31958.4395-1.77937.5816-0.11730.20070.449-0.1744-0.023-0.2566-0.22710.2660.14020.087-0.03170.00310.0479-0.00140.06747.388854.406346.8424
36.4451-5.73255.784917.1509-3.62511.38830.15820.51050.2445-1.41740.022-0.2725-0.14220.6225-0.18020.1673-0.0520.08870.2975-0.01320.219913.809551.379140.8614
431.0296-28.406420.206531.0604-12.981519.23161.03620.4494-1.38630.5484-0.97991.95172.3396-0.459-0.05630.5464-0.28660.26390.3499-0.17440.44753.611930.282838.3254
55.953-0.6355-2.10064.88111.539710.3767-0.1085-0.0201-0.25390.11620.09360.14930.45970.20490.01490.04850.0228-0.0290.0171-0.00170.076910.591837.361738.8937
69.45271.1978-1.1182.48047.009828.450.13410.32370.66560.2085-0.00980.4189-0.5523-1.0312-0.12430.22340.16610.20450.1730.09270.35482.99243.415439.6848
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A149 - 153
2X-RAY DIFFRACTION2A154 - 194
3X-RAY DIFFRACTION3A195 - 203
4X-RAY DIFFRACTION4B149 - 153
5X-RAY DIFFRACTION5B154 - 194
6X-RAY DIFFRACTION6B195 - 203

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