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- PDB-1jr7: CRYSTAL STRUCTURE OF GAB REVEALS OXIDOREDUCTASE FOLD -

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Basic information

Entry
Database: PDB / ID: 1jr7
TitleCRYSTAL STRUCTURE OF GAB REVEALS OXIDOREDUCTASE FOLD
ComponentsHYPOTHETICAL 37.4 KDA PROTEIN IN ILEY-GABD INTERGENIC REGION
KeywordsOXIDOREDUCTASE / LYASE / GAMMA AMINO-BUTYRIC ACID METABOLISM / GABA / FERROUS OXYGENASE / 2-OXOGLUTARATE / ANTIBIOTICS BIOSYNTHESIS / OXYGENASE / B-LACTAM / STRUCTURAL GENOMICS / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


response to carbon starvation / glutarate dioxygenase / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, with 2-oxoglutarate as one donor, and the other dehydrogenated / glutarate dioxygenase activity / L-lysine catabolic process / ferrous iron binding / iron ion binding / protein-containing complex / identical protein binding
Similarity search - Function
Glutarate 2-hydroxylase GlaH / CsiD / : / Clavaminate synthase-like / Double-stranded beta-helix / Taurine dioxygenase TauD-like superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Glutarate 2-hydroxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2 Å
AuthorsLima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Protein Sci. / Year: 2002
Title: Structural genomics: a pipeline for providing structures for the biologist.
Authors: Chance, M.R. / Bresnick, A.R. / Burley, S.K. / Jiang, J.S. / Lima, C.D. / Sali, A. / Almo, S.C. / Bonanno, J.B. / Buglino, J.A. / Boulton, S. / Chen, H. / Eswar, N. / He, G. / Huang, R. / ...Authors: Chance, M.R. / Bresnick, A.R. / Burley, S.K. / Jiang, J.S. / Lima, C.D. / Sali, A. / Almo, S.C. / Bonanno, J.B. / Buglino, J.A. / Boulton, S. / Chen, H. / Eswar, N. / He, G. / Huang, R. / Ilyin, V. / McMahan, L. / Pieper, U. / Ray, S. / Vidal, M. / Wang, L.K.
History
DepositionAug 12, 2001Deposition site: RCSB / Processing site: RCSB
SupersessionAug 22, 2001ID: 1JFY
Revision 1.0Aug 22, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 8, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYPOTHETICAL 37.4 KDA PROTEIN IN ILEY-GABD INTERGENIC REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0312
Polymers35,9751
Non-polymers561
Water5,765320
1
A: HYPOTHETICAL 37.4 KDA PROTEIN IN ILEY-GABD INTERGENIC REGION
hetero molecules

A: HYPOTHETICAL 37.4 KDA PROTEIN IN ILEY-GABD INTERGENIC REGION
hetero molecules

A: HYPOTHETICAL 37.4 KDA PROTEIN IN ILEY-GABD INTERGENIC REGION
hetero molecules

A: HYPOTHETICAL 37.4 KDA PROTEIN IN ILEY-GABD INTERGENIC REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,1228
Polymers143,8994
Non-polymers2234
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area6840 Å2
ΔGint-84 kcal/mol
Surface area54680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.479, 120.479, 136.604
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein HYPOTHETICAL 37.4 KDA PROTEIN IN ILEY-GABD INTERGENIC REGION / GABT PROTEIN


Mass: 35974.762 Da / Num. of mol.: 1 / Fragment: N-TERMINAL TRUNCATION NDELTA14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: GAB; YGAT / Plasmid: PET28B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P76621
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 3.44 Å3/Da / Density % sol: 64.28 %
Crystal growpH: 5.6 / Details: pH 5.60
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 5.6
Components of the solutions
*PLUS
IDCommon nameCrystal-IDSol-ID
1ammonium sulfate1reservoir
2sodium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9878
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 1, 2001
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9878 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 33216 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 19
Reflection shellResolution: 2→2.07 Å / Redundancy: 3 % / Rmerge(I) obs: 0.238 / % possible all: 94
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Observed criterion σ(I): 0 / Redundancy: 5 % / Num. measured all: 442770 / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
% possible obs: 94.1 % / Mean I/σ(I) obs: 4.2

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Processing

Software
NameClassification
SOLVEphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2→20 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1677 5.3 %RANDOM
Rwork0.193 ---
obs-31483 --
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2490 0 1 320 2811
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.193 / Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.8

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