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- PDB-4njn: Crystal Structure of E.coli GlpG at pH 4.5 -

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Basic information

Entry
Database: PDB / ID: 4njn
TitleCrystal Structure of E.coli GlpG at pH 4.5
ComponentsRhomboid protease GlpG
KeywordsHYDROLASE/MEMBRANE PROTEIN / RHOMBOID PROTEASE / INTRAMEMBRANE PROTEOLYSIS / MEMBRANE PROTEIN / HYDROLASE-MEMBRANE PROTEIN complex
Function / homology
Function and homology information


rhomboid protease / endopeptidase activity / serine-type endopeptidase activity / proteolysis / identical protein binding / plasma membrane
Similarity search - Function
Rhomboid-like fold / Rhomboid-like / Peptidase S54, GlpG peptidase, N-terminal / Rhomboid protease GlpG / GlpG peptidase, N-terminal domain superfamily / Cytoplasmic N-terminal domain of rhomboid serine protease / Peptidase S54, rhomboid domain / Rhomboid family / Rhomboid-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Rhomboid protease GlpG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDickey, S.W. / Baker, R.P. / Cho, S. / Urban, S.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: Proteolysis inside the Membrane Is a Rate-Governed Reaction Not Driven by Substrate Affinity.
Authors: Dickey, S.W. / Baker, R.P. / Cho, S. / Urban, S.
History
DepositionNov 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rhomboid protease GlpG


Theoretical massNumber of molelcules
Total (without water)23,8161
Polymers23,8161
Non-polymers00
Water90150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Rhomboid protease GlpG

A: Rhomboid protease GlpG


Theoretical massNumber of molelcules
Total (without water)47,6322
Polymers47,6322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
Buried area2390 Å2
ΔGint-24 kcal/mol
Surface area16670 Å2
MethodPISA
3
A: Rhomboid protease GlpG
x 6


Theoretical massNumber of molelcules
Total (without water)142,8976
Polymers142,8976
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area11300 Å2
ΔGint-122 kcal/mol
Surface area45860 Å2
MethodPISA
4
A: Rhomboid protease GlpG

A: Rhomboid protease GlpG

A: Rhomboid protease GlpG


Theoretical massNumber of molelcules
Total (without water)71,4483
Polymers71,4483
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area4660 Å2
ΔGint-53 kcal/mol
Surface area23920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.680, 110.680, 127.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Rhomboid protease GlpG / Intramembrane serine protease


Mass: 23816.133 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 87-276
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: glpG, b3424, JW5687 / Production host: Escherichia coli (E. coli) / References: UniProt: P09391, rhomboid protease
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 3.16 Å3/Da / Density % sol: 61.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 3M NaCl, 0.1M Sodium acetate, 10% Glycerol, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9181
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9181 Å / Relative weight: 1
ReflectionResolution: 2.28→44.91 Å / Num. obs: 9974 / % possible obs: 99.7 % / Observed criterion σ(I): 2
Reflection shellResolution: 2.28→2.32 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IC8

2ic8


Resolution: 2.4→44.91 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.908 / SU B: 6.591 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.364 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24765 478 5 %RANDOM
Rwork0.19583 ---
obs0.19833 9029 79.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.531 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å2-1.71 Å2-0 Å2
2---1.71 Å20 Å2
3---5.53 Å2
Refinement stepCycle: LAST / Resolution: 2.4→44.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1451 0 0 50 1501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191501
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9651.9242043
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0985181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.2322.20359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.95415233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.34156
X-RAY DIFFRACTIONr_chiral_restr0.1260.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211127
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 23 -
Rwork0.259 389 -
obs--47.85 %

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