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- PDB-1zxj: Crystal structure of the hypthetical Mycoplasma protein, MPN555 -

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Basic information

Entry
Database: PDB / ID: 1zxj
TitleCrystal structure of the hypthetical Mycoplasma protein, MPN555
ComponentsHypothetical protein MG377 homologHypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / mostly alpha helical protein / tri-lobal structure / PSI / Protein Structure Initiative / Berkeley Structural Genomics Center / BSGC
Function / homologyTrigger factor, domain 2 / Trigger factor, C-terminal domain / Trigger factor, C-terminal domain superfamily / Trigger factor/SurA domain superfamily / protein transport / protein folding / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein MG377 homolog
Function and homology information
Biological speciesMycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsSchulze-Gahmen, U. / Aono, S. / Shengfeng, C. / Yokota, H. / Kim, R. / Kim, S.-H. / Berkeley Structural Genomics Center (BSGC)
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of the hypothetical Mycoplasma protein MPN555 suggests a chaperone function.
Authors: Schulze-Gahmen, U. / Aono, S. / Chen, S. / Yokota, H. / Kim, R. / Kim, S.H.
History
DepositionJun 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 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: Hypothetical protein MG377 homolog
B: Hypothetical protein MG377 homolog
C: Hypothetical protein MG377 homolog
D: Hypothetical protein MG377 homolog


Theoretical massNumber of molelcules
Total (without water)101,8084
Polymers101,8084
Non-polymers00
Water25214
1
A: Hypothetical protein MG377 homolog


Theoretical massNumber of molelcules
Total (without water)25,4521
Polymers25,4521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hypothetical protein MG377 homolog


Theoretical massNumber of molelcules
Total (without water)25,4521
Polymers25,4521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hypothetical protein MG377 homolog


Theoretical massNumber of molelcules
Total (without water)25,4521
Polymers25,4521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Hypothetical protein MG377 homolog


Theoretical massNumber of molelcules
Total (without water)25,4521
Polymers25,4521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
C: Hypothetical protein MG377 homolog

C: Hypothetical protein MG377 homolog

D: Hypothetical protein MG377 homolog

D: Hypothetical protein MG377 homolog


Theoretical massNumber of molelcules
Total (without water)101,8084
Polymers101,8084
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation1_454x-1,y,z-11
crystal symmetry operation2_656-x+1,y,-z+11
Buried area9380 Å2
ΔGint-58 kcal/mol
Surface area39410 Å2
MethodPISA
6
A: Hypothetical protein MG377 homolog
B: Hypothetical protein MG377 homolog

A: Hypothetical protein MG377 homolog
B: Hypothetical protein MG377 homolog


Theoretical massNumber of molelcules
Total (without water)101,8084
Polymers101,8084
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area8480 Å2
ΔGint-54 kcal/mol
Surface area39270 Å2
MethodPISA
7
C: Hypothetical protein MG377 homolog

D: Hypothetical protein MG377 homolog


Theoretical massNumber of molelcules
Total (without water)50,9042
Polymers50,9042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3040 Å2
ΔGint-22 kcal/mol
Surface area21360 Å2
MethodPISA
8
A: Hypothetical protein MG377 homolog

B: Hypothetical protein MG377 homolog


Theoretical massNumber of molelcules
Total (without water)50,9042
Polymers50,9042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2640 Å2
ΔGint-20 kcal/mol
Surface area21240 Å2
MethodPISA
9
B: Hypothetical protein MG377 homolog

B: Hypothetical protein MG377 homolog


Theoretical massNumber of molelcules
Total (without water)50,9042
Polymers50,9042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area1570 Å2
ΔGint-10 kcal/mol
Surface area21730 Å2
MethodPISA
10
D: Hypothetical protein MG377 homolog

D: Hypothetical protein MG377 homolog


Theoretical massNumber of molelcules
Total (without water)50,9042
Polymers50,9042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area1610 Å2
ΔGint-7 kcal/mol
Surface area22470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.370, 45.590, 153.930
Angle α, β, γ (deg.)90.00, 111.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Hypothetical protein MG377 homolog / Hypothesis / MPN555


Mass: 25451.900 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
Plasmid: pSKB3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pSJS1244 / References: UniProt: P75223
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.13 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Bis/Tris, ammonium sulfate, pentaerythritol ethoxylate, zwittergent 3-14, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 7, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→42.76 Å / Num. all: 41240 / Num. obs: 38935 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 54.3 Å2 / Limit h max: 47 / Limit h min: 0 / Limit k max: 16 / Limit k min: 0 / Limit l max: 50 / Limit l min: -54 / Observed criterion F max: 1848136.33 / Observed criterion F min: 13 / Rsym value: 0.079 / Net I/σ(I): 6.7
Reflection shellResolution: 2.8→2.95 Å / % possible all: 91.5

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→19.81 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.322 2840 7.3 %random
Rwork0.248 ---
all-41128 --
obs-38842 94.4 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 33.5698 Å2 / ksol: 0.313832 e/Å3
Displacement parametersBiso max: 99.89 Å2 / Biso mean: 50.04 Å2 / Biso min: 6.49 Å2
Baniso -1Baniso -2Baniso -3
1-6 Å20 Å22.62 Å2
2---7.97 Å20 Å2
3---1.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.37 Å
Luzzati d res high-2.8
Refinement stepCycle: LAST / Resolution: 2.8→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5898 0 0 14 5912
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_improper_angle_d0.72
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.8-2.930.3893197.20.33141240.0225122444386.7
2.93-3.080.3523337.30.30442520.0195170458588.7
3.08-3.270.3673367.10.27943940.025155473091.7
3.27-3.520.363096.40.27545440.025171485393.9
3.52-3.880.34239680.24645610.0175107495797.1
3.88-4.430.2723917.70.21846780.0145121506999
4.43-5.560.3173837.50.2247540.0165160513799.6
5.56-19.810.2913737.40.23846950.0155137506898.7

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