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- PDB-2g6t: Crystal structure of an uncharacterized protein from Clostridium ... -

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Basic information

Entry
Database: PDB / ID: 2g6t
TitleCrystal structure of an uncharacterized protein from Clostridium acetobutylicum
ComponentsUncharacterized protein, homolog HI1244 from Haemophilus influenzae
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Hypothetical protein / Clostridium acetobutylicum / T1230 / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Protein of unknown function DUF1919 / CAC2185-like superfamily / : / Domain of unknown function (DUF1919) / C2185-like, N-terminal / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Uncharacterized protein, homolog HI1244 from Haemophilus influenzae
Similarity search - Component
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsRao, K.N. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of an uncharacterized protein from Clostridium acetobutylicum
Authors: Rao, K.N. / Swaminathan, S.
History
DepositionFeb 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE EXTRA DENSITY AT THE C-TERMINUS WAS MODELED AS UNK (UNKNOWN RESIDUE).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein, homolog HI1244 from Haemophilus influenzae
B: Uncharacterized protein, homolog HI1244 from Haemophilus influenzae


Theoretical massNumber of molelcules
Total (without water)73,5002
Polymers73,5002
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-16 kcal/mol
Surface area27550 Å2
MethodPISA
2
A: Uncharacterized protein, homolog HI1244 from Haemophilus influenzae
B: Uncharacterized protein, homolog HI1244 from Haemophilus influenzae

A: Uncharacterized protein, homolog HI1244 from Haemophilus influenzae
B: Uncharacterized protein, homolog HI1244 from Haemophilus influenzae


Theoretical massNumber of molelcules
Total (without water)147,0004
Polymers147,0004
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_566x,x-y+1,-z+7/61
Buried area10060 Å2
ΔGint-40 kcal/mol
Surface area49420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.970, 123.970, 254.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Uncharacterized protein, homolog HI1244 from Haemophilus influenzae


Mass: 36749.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Production host: Escherichia coli (E. coli) / References: GenBank: 15025180, UniProt: Q97H28*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.84 Å3/Da / Density % sol: 67.99 %
Crystal growTemperature: 293 K / pH: 7.5
Details: PEG 8000, Ethylene Glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 13, 2005 / Details: MIRRORS
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 23984 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 32.6 % / Biso Wilson estimate: 42 Å2 / Rmerge(I) obs: 0.152 / Rsym value: 0.152 / Net I/σ(I): 7.3
Reflection shellResolution: 3→3.11 Å / Redundancy: 24.2 % / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data scaling
SHELXDphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 3→46 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 29873.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The atoms listed in remark 470 were not modeled due to lack of electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 674 2.9 %RANDOM
Rwork0.213 ---
all0.248 23111 --
obs0.213 23111 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.9552 Å2 / ksol: 0.398683 e/Å3
Displacement parametersBiso mean: 37.8 Å2
Baniso -1Baniso -2Baniso -3
1--4.42 Å24.55 Å20 Å2
2---4.42 Å20 Å2
3---8.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 3→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5005 0 0 51 5056
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it2.182
X-RAY DIFFRACTIONc_scbond_it2.582
X-RAY DIFFRACTIONc_scangle_it3.452.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.334 96 2.7 %
Rwork0.3 3465 -
obs--91.9 %

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