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- PDB-4lrj: Bacterial Effector NleH1 Kinase Domain with AMPPNP and Mg2+ -

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Basic information

Entry
Database: PDB / ID: 4lrj
TitleBacterial Effector NleH1 Kinase Domain with AMPPNP and Mg2+
ComponentsEffector NleH1
KeywordsTRANSFERASE / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / kinase fold / baterial effector kinase
Function / homology
Function and homology information


: / protein autophosphorylation / protein phosphorylation / nucleotide binding
Similarity search - Function
Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / T3SS effector protein NleH
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.619 Å
AuthorsCygler, M. / Grishin, A.M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: Structure / Year: 2014
Title: NleH defines a new family of bacterial effector kinases.
Authors: Grishin, A.M. / Cherney, M. / Anderson, D.H. / Phanse, S. / Babu, M. / Cygler, M.
History
DepositionJul 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _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_asym_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_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

Downloads & links

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Assembly

Deposited unit
A: Effector NleH1
B: Effector NleH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6458
Polymers37,5352
Non-polymers1,1106
Water5,098283
1
A: Effector NleH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3475
Polymers18,7681
Non-polymers5794
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Effector NleH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2983
Polymers18,7681
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.698, 98.205, 40.774
Angle α, β, γ (deg.)90.00, 96.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Effector NleH1


Mass: 18767.713 Da / Num. of mol.: 2 / Fragment: Kinase Domain (UNP residues 128-293)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 EDL933 / Gene: ECs0848, nleh1, Z0989 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star
References: UniProt: Q8X831, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM Tris 8.5, 20% PEG 3350, 100 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77.2 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jan 8, 2013
RadiationMonochromator: dcm WITH CRYO-COOLED 1ST CRYSTAL SAGITALLY BENT 2ND CRYSTAL FOLLOWED BY VERTICALLY FOCUSING MIRROR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
Reflection twinOperator: l,-k,h / Fraction: 0.26
ReflectionResolution: 1.61→50 Å / Num. obs: 41051 / % possible obs: 99.7 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 21.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.61-1.645.30.338195.7
1.64-1.675.60.3021100
1.67-1.75.60.2551100
1.7-1.735.70.2271100
1.73-1.775.70.181100
1.77-1.815.70.1581100
1.81-1.865.70.1311100
1.86-1.915.70.111100
1.91-1.975.70.0871100
1.97-2.035.70.0791100
2.03-2.15.70.0751100
2.1-2.195.70.0731100
2.19-2.285.70.0681100
2.28-2.45.70.061100
2.4-2.565.70.054199.8
2.56-2.755.70.0541100
2.75-3.035.80.061100
3.03-3.475.80.0521100
3.47-4.375.80.0431100
4.37-505.60.041199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 50.51 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å31.26 Å
Translation2.5 Å31.26 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.3_1477refinement
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MxDCdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.619→31.256 Å / Occupancy max: 1 / Occupancy min: 0.3 / σ(F): 1.35 / Phase error: 25.28 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1875 1999 4.96 %
Rwork0.1601 --
obs0.1624 40331 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.851 Å2
Refinement stepCycle: LAST / Resolution: 1.619→31.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2458 0 66 283 2807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062609
X-RAY DIFFRACTIONf_angle_d0.9973547
X-RAY DIFFRACTIONf_dihedral_angle_d17.953987
X-RAY DIFFRACTIONf_chiral_restr0.064397
X-RAY DIFFRACTIONf_plane_restr0.003456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6196-1.66010.26191350.26972651X-RAY DIFFRACTION92
1.6601-1.7050.32021440.27152768X-RAY DIFFRACTION95
1.705-1.75510.25941410.26042710X-RAY DIFFRACTION95
1.7551-1.81180.28811430.24992711X-RAY DIFFRACTION95
1.8118-1.87650.26591390.23632733X-RAY DIFFRACTION95
1.8765-1.95150.24891370.22212754X-RAY DIFFRACTION95
1.9515-2.04030.20991430.20952755X-RAY DIFFRACTION95
2.0403-2.14770.21321450.20492739X-RAY DIFFRACTION95
2.1477-2.28210.20161450.18882713X-RAY DIFFRACTION95
2.2821-2.45810.1991400.18022730X-RAY DIFFRACTION95
2.4581-2.70490.18021440.1682777X-RAY DIFFRACTION95
2.7049-3.09510.21421410.1532725X-RAY DIFFRACTION95
3.0951-3.8950.18461460.1142756X-RAY DIFFRACTION95
3.895-20.26510.11161520.10472788X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0760.0401-0.03190.17240.0270.2816-0.0313-0.0055-0.01470.0085-0.01560.0008-0.0111-0.0465-00.13340.008-0.01030.1382-0.00910.1297-13.6770.3603-8.8415
20.18530.09910.03730.1573-0.04620.06130.1113-0.0432-0.07830.0488-0.0441-0.03230.0048-0.0100.1703-0.00640.00390.1322-0.00690.1707-5.385424.8983-25.9953
30.00660.0178-0.0150.0526-0.04610.04830.0220.00610.01970.00730.0167-0.0097-0.01010.00420.01690.2863-0.1156-0.00360.287-0.00720.3643-11.213129.9821-26.9391
40.09610.0490.0710.07750.03660.0529-0.01030.0039-0.01640.008-0.0280.0253-0.0049-0.0467-0.03360.31360.01790.08640.1987-0.04960.1842-12.3845.6329-14.574
50.04360.0205-0.06450.0476-0.0310.07080.0043-0.00310.00460.0181-0.0012-0.01060.0027-0.0117-00.1906-0.0073-0.01220.175-0.00880.1912-9.81611.7003-16.2118
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 131:293 )A131 - 293
2X-RAY DIFFRACTION2( CHAIN B AND RESID 132:293 )B132 - 293
3X-RAY DIFFRACTION3( CHAIN B AND RESID 301:301 )B301
4X-RAY DIFFRACTION4( CHAIN A AND RESID 301:301 )A301
5X-RAY DIFFRACTION5( CHAIN A AND RESID 401:561 ) OR ( CHAIN B AND RESID 401:522 )A401 - 561
6X-RAY DIFFRACTION5( CHAIN A AND RESID 401:561 ) OR ( CHAIN B AND RESID 401:522 )B401 - 522

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