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- PDB-1xef: Crystal structure of the ATP/Mg2+ bound composite dimer of HlyB-NBD -

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Basic information

Entry
Database: PDB / ID: 1xef
TitleCrystal structure of the ATP/Mg2+ bound composite dimer of HlyB-NBD
ComponentsAlpha-hemolysin translocation ATP-binding protein hlyB
KeywordsTRANSPORT PROTEIN / ABC-transporter / ATPase / Haemolysin B / ATP-dependent transport protein
Function / homology
Function and homology information


protein secretion by the type I secretion system / type I protein secretion system complex / toxin transmembrane transporter activity / secretion by cell / toxin transport / ABC-type transporter activity / peptidase activity / integral component of membrane / ATP binding / plasma membrane
Similarity search - Function
Peptidase C39-like A / ATPase, type I secretion system, HlyB / Peptidase C39 family / Peptidase C39, bacteriocin processing / Peptidase family C39 domain profile. / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily ...Peptidase C39-like A / ATPase, type I secretion system, HlyB / Peptidase C39 family / Peptidase C39, bacteriocin processing / Peptidase family C39 domain profile. / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporters family signature. / ABC transporter-like, conserved site / ABC transporter / ATP-binding cassette, ABC transporter-type domain profile. / ABC transporter-like, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Alpha-hemolysin translocation ATP-binding protein HlyB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZaitseva, J. / Jenewein, S. / Holland, I.B. / Schmitt, L.
CitationJournal: Embo J. / Year: 2005
Title: H662 is the linchpin of ATP hydrolysis in the nucleotide-binding domain of the ABC transporter HlyB
Authors: Zaitseva, J. / Jenewein, S. / Jumpertz, T. / Holland, I.B. / Schmitt, L.
History
DepositionSep 10, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_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.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_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_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: Alpha-hemolysin translocation ATP-binding protein hlyB
B: Alpha-hemolysin translocation ATP-binding protein hlyB
C: Alpha-hemolysin translocation ATP-binding protein hlyB
D: Alpha-hemolysin translocation ATP-binding protein hlyB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,55412
Polymers107,4284
Non-polymers2,1268
Water3,099172
1
A: Alpha-hemolysin translocation ATP-binding protein hlyB
B: Alpha-hemolysin translocation ATP-binding protein hlyB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7776
Polymers53,7142
Non-polymers1,0634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-38 kcal/mol
Surface area22030 Å2
MethodPISA
2
C: Alpha-hemolysin translocation ATP-binding protein hlyB
D: Alpha-hemolysin translocation ATP-binding protein hlyB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7776
Polymers53,7142
Non-polymers1,0634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-37 kcal/mol
Surface area22180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.926, 194.917, 63.706
Angle α, β, γ (deg.)90.00, 110.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Alpha-hemolysin translocation ATP-binding protein hlyB / HlyB


Mass: 26856.898 Da / Num. of mol.: 4 / Fragment: HlyB-NBD(residues 467-707) / Mutation: H662A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pPSG116 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P08716
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.3 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: Sodium acetate, isopropanol, PEG-MME 5500, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.5→95.35 Å / Num. all: 33496 / Num. obs: 33295 / % possible obs: 99.38 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rsym value: 0.053 / Net I/σ(I): 23.4
Reflection shellResolution: 2.5→2.56 Å / Mean I/σ(I) obs: 2.8 / Rsym value: 0.401 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MT0
Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.906 / SU B: 22.41 / SU ML: 0.271 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): 2.8 / ESU R: 1.141 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26426 1761 5 %RANDOM
Rwork0.21944 ---
all0.22177 34986 --
obs0.22177 33295 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51.109 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å2-0.4 Å2
2--3.05 Å20 Å2
3----2.93 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7552 0 128 172 7852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0227788
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0371.99210540
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2185960
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.95424.138348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.188151432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.361564
X-RAY DIFFRACTIONr_chiral_restr0.0640.21208
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025720
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1790.23539
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.25323
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2301
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0920.28
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0860.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2351.54934
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.42527708
X-RAY DIFFRACTIONr_scbond_it0.27633204
X-RAY DIFFRACTIONr_scangle_it0.5074.52832
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 126 -
Rwork0.313 2429 -
obs--99.77 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.4237-0.3503-0.19112.2912-0.10875.7636-0.02510.2523-0.3377-0.16270.04640.00040.18880.1758-0.0213-0.1676-0.0345-0.0142-0.1105-0.0502-0.09413.342-1.46-12.098
23.40153.5608-0.95199.51960.920110.6477-0.42530.2568-0.27530.38610.1393-0.08141.4842-0.29510.28610.19860.03510.0383-0.2929-0.08310.1273-2.79-19.1425.483
31.81840.4502-0.47881.8688-1.56295.4570.0679-0.37340.06820.1812-0.1624-0.1578-0.08670.47410.0945-0.0826-0.034-0.0421-0.0457-0.0051-0.05122.612.6620.64
44.6912-2.1096-0.48379.70592.27435.53370.131-0.0336-0.0860.1318-0.22170.4222-0.1211-0.63410.0908-0.10460.01550.0175-0.16490.0181-0.0456-12.04914.4743.488
52.58240.1520.43142.6527-0.04115.7616-0.0292-0.2340.30420.21380.0602-0.0932-0.24530.3024-0.0309-0.1709-0.001-0.026-0.1222-0.0345-0.073625.71147.18313.304
66.2167-5.5318-0.104713.5448-0.14135.8207-0.1513-0.35330.2805-0.15850.0518-0.3102-0.8708-0.25160.09960.0951-0.03730.0221-0.3832-0.0480.106518.71264.588-4.196
71.72090.0205-0.04591.9149-1.62296.05630.08830.4641-0.0972-0.2259-0.1915-0.17540.2160.46220.1032-0.06750.05790.0090.01310.0128-0.036225.04543.056-19.403
85.71213.1446-0.56479.26031.96335.53410.00560.07350.2095-0.2109-0.20740.54670.1892-0.5260.2018-0.0707-0.0108-0.0564-0.18620.0118-0.008410.44631.187-2.303
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA467 - 5491 - 83
2X-RAY DIFFRACTION1AA624 - 707158 - 241
3X-RAY DIFFRACTION2AA550 - 62384 - 157
4X-RAY DIFFRACTION3BB467 - 5491 - 83
5X-RAY DIFFRACTION3BB624 - 707158 - 241
6X-RAY DIFFRACTION4BB550 - 62384 - 157
7X-RAY DIFFRACTION5CC467 - 5491 - 83
8X-RAY DIFFRACTION5CC624 - 707158 - 241
9X-RAY DIFFRACTION6CC550 - 62384 - 157
10X-RAY DIFFRACTION7DD467 - 5491 - 83
11X-RAY DIFFRACTION7DD624 - 707158 - 241
12X-RAY DIFFRACTION8DD550 - 62384 - 157

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