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- PDB-4q3j: Crystal structure of NFkB-p65-degrading zinc protease family protein -

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Basic information

Entry
Database: PDB / ID: 4q3j
TitleCrystal structure of NFkB-p65-degrading zinc protease family protein
ComponentsNFkB-p65-degrading zinc protease family protein
KeywordsHYDROLASE / alpha beta / cytosol
Function / homology:
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.862 Å
AuthorsSousa, M.C. / Turco, M.M.
CitationJournal: Biochemistry / Year: 2014
Title: The Structure and Specificity of the Type III Secretion System Effector NleC Suggest a DNA Mimicry Mechanism of Substrate Recognition.
Authors: Turco, M.M. / Sousa, M.C.
History
DepositionApr 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NFkB-p65-degrading zinc protease family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4793
Polymers37,3891
Non-polymers902
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.205, 67.480, 81.688
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NFkB-p65-degrading zinc protease family protein


Mass: 37388.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: Sakai / Gene: S1M_1031 / Production host: Escherichia coli (E. coli) / References: UniProt: U1C6A4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 1.67 Å3/Da / Density % sol: 26.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10% PEG-3350, 50 mM Mg(CHO2)2, 0.1 M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.2574,1.2831,1.2835
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 6, 2011
RadiationMonochromator: crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.25741
21.28311
31.28351
ReflectionResolution: 1.862→50 Å / Num. all: 21559 / Num. obs: 19840 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.autosol: 1.7.1_743)model building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7.1_743phasing
RefinementMethod to determine structure: MAD / Resolution: 1.862→34.942 Å / SU ML: 0.45 / σ(F): 0 / Phase error: 22.18 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2181 1905 9.6 %Random
Rwork0.1795 ---
obs0.1833 19840 91.98 %-
all-21559 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.619 Å2 / ksol: 0.364 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.9042 Å2-0 Å20 Å2
2---5.6521 Å2-0 Å2
3---6.5563 Å2
Refinement stepCycle: LAST / Resolution: 1.862→34.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2067 0 2 186 2255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142116
X-RAY DIFFRACTIONf_angle_d0.9932877
X-RAY DIFFRACTIONf_dihedral_angle_d13.103786
X-RAY DIFFRACTIONf_chiral_restr0.07307
X-RAY DIFFRACTIONf_plane_restr0.003388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8619-1.90850.41171090.32011051X-RAY DIFFRACTION77
1.9085-1.960.31281190.2541173X-RAY DIFFRACTION85
1.96-2.01770.27491330.21491254X-RAY DIFFRACTION92
2.0177-2.08280.28321370.22081273X-RAY DIFFRACTION92
2.0828-2.15730.23341430.18561316X-RAY DIFFRACTION96
2.1573-2.24360.27171350.21071275X-RAY DIFFRACTION93
2.2436-2.34570.25091370.18361295X-RAY DIFFRACTION94
2.3457-2.46940.25291410.18131328X-RAY DIFFRACTION96
2.4694-2.6240.20191440.16541342X-RAY DIFFRACTION96
2.624-2.82650.19351410.16881346X-RAY DIFFRACTION96
2.8265-3.11080.20581410.1741309X-RAY DIFFRACTION95
3.1108-3.56060.22241420.1671323X-RAY DIFFRACTION94
3.5606-4.48450.19021410.14731317X-RAY DIFFRACTION92
4.4845-34.9480.14951420.16341333X-RAY DIFFRACTION88
Refinement TLS params.Method: refined / Origin x: 8.0022 Å / Origin y: 28.7335 Å / Origin z: 51.6032 Å
111213212223313233
T0.0758 Å2-0.0121 Å2-0.0077 Å2-0.1292 Å20.0055 Å2--0.097 Å2
L1.1147 °2-0.3549 °2-0.3603 °2-2.1839 °20.7131 °2--1.1421 °2
S0.0165 Å °-0.0449 Å °-0.0019 Å °0.0744 Å °0.0148 Å °-0.1152 Å °-0.0148 Å °0.0745 Å °-0.0032 Å °
Refinement TLS groupSelection details: all

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