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- PDB-2p90: The crystal structure of a protein of unknown function from Coryn... -

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Basic information

Entry
Database: PDB / ID: 2p90
TitleThe crystal structure of a protein of unknown function from Corynebacterium glutamicum ATCC 13032
ComponentsHypothetical protein Cgl1923
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Corynebacterium glutamicum / PSI-2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


Rv2714-like / PAC-like subunit / Helix Hairpins - #100 / Proteasome assembly chaperone 2 / Proteasome assembly chaperone 2 superfamily / PAC2 family / Helix Hairpins / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Rv2714-like / PAC-like subunit / Helix Hairpins - #100 / Proteasome assembly chaperone 2 / Proteasome assembly chaperone 2 superfamily / PAC2 family / Helix Hairpins / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsZhang, R. / Duggan, E. / Gu, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a protein of unknown function from Corynebacterium glutamicum ATCC 13032
Authors: Zhang, R. / Duggan, E. / Gu, M. / Joachimiak, A.
History
DepositionMar 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein Cgl1923
B: Hypothetical protein Cgl1923
C: Hypothetical protein Cgl1923


Theoretical massNumber of molelcules
Total (without water)105,8653
Polymers105,8653
Non-polymers00
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-21 kcal/mol
Surface area37000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.834, 113.348, 117.368
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThis protein existed as trimer. The deposited molecules A,B,C represents the trimer in the asymmetric unit.

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Components

#1: Protein Hypothetical protein Cgl1923


Mass: 35288.176 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Species: Corynebacterium glutamicum / Strain: DSM 20300, JCM 1318, LMG 3730, NCIMB 10025 / Gene: Cgl1923, cg2106 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8NP93
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.66 Å3/Da / Density % sol: 53.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Li2SO4, 0.1M HEPES, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2007 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.35→81.65 Å / Num. all: 45418 / Num. obs: 45314 / % possible obs: 99.77 % / Observed criterion σ(I): 2 / Redundancy: 17.9 % / Biso Wilson estimate: 51 Å2 / Rmerge(I) obs: 0.142 / Net I/σ(I): 24
Reflection shellResolution: 2.35→2.411 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.807 / Mean I/σ(I) obs: 1.925 / % possible all: 99.28

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→81.65 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.926 / SU ML: 0.159 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.274 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25119 2420 5.1 %RANDOM
Rwork0.19322 ---
obs0.19617 45314 99.77 %-
all-45314 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.31 Å20 Å20 Å2
2---2.81 Å20 Å2
3---1.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.049 Å0.048 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.35→81.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6269 0 0 326 6595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0216407
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.9738716
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7575805
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64124.467300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.671151080
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8931545
X-RAY DIFFRACTIONr_chiral_restr0.110.21000
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024885
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.22890
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.24254
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2399
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.266
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9411.54152
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.62926542
X-RAY DIFFRACTIONr_scbond_it2.47432498
X-RAY DIFFRACTIONr_scangle_it3.9914.52174
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 162 -
Rwork0.24 3299 -
obs--99.28 %
Refinement TLS params.Method: refined / Origin x: 28.5546 Å / Origin y: 42.7201 Å / Origin z: 34.2704 Å
111213212223313233
T-0.0049 Å2-0.015 Å2-0.0154 Å2--0.0379 Å20.0235 Å2---0.0221 Å2
L0.2447 °20.0279 °2-0.1258 °2-0.139 °20.0062 °2--0.1718 °2
S0.0225 Å °0.0011 Å °-0.0501 Å °-0.0021 Å °-0.0239 Å °-0.0303 Å °-0.0014 Å °-0.0278 Å °0.0014 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 506 - 50
2X-RAY DIFFRACTION1AA51 - 10051 - 100
3X-RAY DIFFRACTION1AA101 - 150101 - 150
4X-RAY DIFFRACTION1AA151 - 200151 - 200
5X-RAY DIFFRACTION1AA201 - 240201 - 240
6X-RAY DIFFRACTION1AA241 - 274241 - 274
7X-RAY DIFFRACTION1BB8 - 508 - 50
8X-RAY DIFFRACTION1BB51 - 10051 - 100
9X-RAY DIFFRACTION1BB101 - 150101 - 150
10X-RAY DIFFRACTION1BB151 - 200151 - 200
11X-RAY DIFFRACTION1BB201 - 240201 - 240
12X-RAY DIFFRACTION1BB241 - 278241 - 278
13X-RAY DIFFRACTION1CC7 - 507 - 50
14X-RAY DIFFRACTION1CC51 - 10051 - 100
15X-RAY DIFFRACTION1CC101 - 150101 - 150
16X-RAY DIFFRACTION1CC151 - 200151 - 200
17X-RAY DIFFRACTION1CC201 - 240201 - 240
18X-RAY DIFFRACTION1CC241 - 274241 - 274

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