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- PDB-3bij: Crystal structure of protein GSU0716 from Geobacter sulfurreducen... -

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Basic information

Entry
Database: PDB / ID: 3bij
TitleCrystal structure of protein GSU0716 from Geobacter sulfurreducens. Northeast Structural Genomics target GsR13
ComponentsUncharacterized protein GSU0716
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


cysteine-type endopeptidase activity / proteolysis / cytoplasm
Similarity search - Function
: / Rossmann fold - #1460 / : / Caspase domain / Caspase-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Peptidase, C14 family
Similarity search - Component
Biological speciesGeobacter sulfurreducens PCA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsForouhar, F. / Neely, H. / Su, M. / Seetharaman, J. / Benach, J. / Conover, K. / Fang, Y. / Xiao, R. / Owen, L.A. / Maglaqui, M. ...Forouhar, F. / Neely, H. / Su, M. / Seetharaman, J. / Benach, J. / Conover, K. / Fang, Y. / Xiao, R. / Owen, L.A. / Maglaqui, M. / Cunningham, K. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of protein GSU0716 from Geobacter sulfurreducens.
Authors: Forouhar, F. / Neely, H. / Su, M. / Seetharaman, J. / Benach, J. / Conover, K. / Fang, Y. / Xiao, R. / Owen, L.A. / Maglaqui, M. / Cunningham, K. / Baran, M.C. / Acton, T.B. / Montelione, G. ...Authors: Forouhar, F. / Neely, H. / Su, M. / Seetharaman, J. / Benach, J. / Conover, K. / Fang, Y. / Xiao, R. / Owen, L.A. / Maglaqui, M. / Cunningham, K. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionNov 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein GSU0716
B: Uncharacterized protein GSU0716
C: Uncharacterized protein GSU0716


Theoretical massNumber of molelcules
Total (without water)94,3423
Polymers94,3423
Non-polymers00
Water2,540141
1
A: Uncharacterized protein GSU0716
B: Uncharacterized protein GSU0716

A: Uncharacterized protein GSU0716
B: Uncharacterized protein GSU0716

A: Uncharacterized protein GSU0716
B: Uncharacterized protein GSU0716

A: Uncharacterized protein GSU0716
B: Uncharacterized protein GSU0716


Theoretical massNumber of molelcules
Total (without water)251,5798
Polymers251,5798
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area23600 Å2
MethodPISA
2
C: Uncharacterized protein GSU0716
x 8


Theoretical massNumber of molelcules
Total (without water)251,5798
Polymers251,5798
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_556-x,y,-z+11
crystal symmetry operation6_556x,-y,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_556-y,-x,-z+11
Buried area24990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.718, 121.718, 219.038
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
DetailsAUTHORS STATE THAT THE OCTAMERIC ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE AT THE TIME OF DEPOSITION.

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Components

#1: Protein Uncharacterized protein GSU0716


Mass: 31447.328 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens PCA (bacteria)
Species: Geobacter sulfurreducens / Strain: PCA, DSM 12127 / Gene: GSU0716, 2687216 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q74F93
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.15 Å3/Da / Density % sol: 42.79 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM NaCl, 5 mM DTT. Reservoir solution: 100 mM Hepes pH 7.5, 1.45 M Na3 Citrate, 20 microgram/mL subtilisin, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 13, 2007 / Details: Mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 54406 / Num. obs: 54406 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.8 % / Biso Wilson estimate: 46.7 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.06 / Net I/σ(I): 42.49
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 4.6 / Num. unique all: 5436 / Rsym value: 0.357 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
MAR345CCDdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SnBphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→19.98 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 435029.32 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used in phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.267 4614 9.9 %RANDOM
Rwork0.207 ---
all0.21 54396 --
obs0.207 46781 86 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.4251 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 51.9 Å2
Baniso -1Baniso -2Baniso -3
1--4.35 Å20 Å20 Å2
2---4.35 Å20 Å2
3---8.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6059 0 0 141 6200
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.348 415 11.4 %
Rwork0.251 3216 -
obs-3216 66.6 %

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