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- PDB-2r6s: Crystal structure of Gab protein -

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Basic information

Entry
Database: PDB / ID: 2r6s
TitleCrystal structure of Gab protein
ComponentsGab protein
KeywordsUNKNOWN FUNCTION / jelly-roll motif
Function / homology
Function and homology information


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 / L-lysine catabolic process / dioxygenase activity / ferrous iron 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 / Resolution: 2.1 Å
AuthorsLohkamp, B. / Dobritzsch, D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: A mixture of fortunes: the curious determination of the structure of Escherichia coli BL21 Gab protein.
Authors: Lohkamp, B. / Dobritzsch, D.
History
DepositionSep 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Feb 8, 2023Group: Database references / Derived calculations / Source and taxonomy
Category: database_2 / entity_src_nat ...database_2 / entity_src_nat / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_nat.pdbx_ncbi_taxonomy_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gab protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,86027
Polymers37,4181
Non-polymers2,44126
Water3,927218
1
A: Gab protein
hetero molecules

A: Gab protein
hetero molecules

A: Gab protein
hetero molecules

A: Gab protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,438108
Polymers149,6734
Non-polymers9,765104
Water724
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 area29090 Å2
ΔGint-312 kcal/mol
Surface area52680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.900, 120.900, 137.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Gab protein


Mass: 37418.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: B-strain / References: UniProt: A2UG88, UniProt: A0A140N6S1*PLUS

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Non-polymers , 5 types, 244 molecules

#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-BCN / BICINE / Bicine


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#5: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 3.35 Å3/Da / Density % sol: 63.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1.6M ammonium sulphate, 0.1M bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 7, 2005 / Details: mirrors
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.1→45.4 Å / Num. all: 29961 / Num. obs: 29931 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 10.5
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.632 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4316 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
ProDCdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementStarting model: PDB ENTRY 1JR7

1jr7


Resolution: 2.1→45.36 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.653 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.199 1520 5.1 %RANDOM
Rwork0.162 ---
all0.163 29931 --
obs0.163 29925 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.974 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å20 Å2
2--1.01 Å20 Å2
3----2.03 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2452 0 153 218 2823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212757
X-RAY DIFFRACTIONr_bond_other_d0.0020.021955
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.9863712
X-RAY DIFFRACTIONr_angle_other_deg0.91734720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1895323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.76923.517145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79815450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6351523
X-RAY DIFFRACTIONr_chiral_restr0.0880.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022957
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02574
X-RAY DIFFRACTIONr_nbd_refined0.2080.2500
X-RAY DIFFRACTIONr_nbd_other0.2030.22080
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21229
X-RAY DIFFRACTIONr_nbtor_other0.090.21450
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2178
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2450.2101
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.217
X-RAY DIFFRACTIONr_mcbond_it1.1071.52010
X-RAY DIFFRACTIONr_mcbond_other0.1851.5614
X-RAY DIFFRACTIONr_mcangle_it1.26922498
X-RAY DIFFRACTIONr_scbond_it1.8531390
X-RAY DIFFRACTIONr_scangle_it2.5524.51202
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 130 -
Rwork0.227 2074 -
all-2204 -
obs--100 %

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