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- PDB-2oap: Crystal structure of the archaeal secretion ATPase GspE in comple... -

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Basic information

Entry
Database: PDB / ID: 2oap
TitleCrystal structure of the archaeal secretion ATPase GspE in complex with AMP-PNP
ComponentsType II secretion system protein
KeywordsHYDROLASE / Hexameric ATPase
Function / homology
Function and homology information


Beta-Lactamase - #380 / Type II/IV secretion system protein / Type II/IV secretion system protein / Beta-Lactamase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Type II secretion system protein (GspE-2)
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.95 Å
AuthorsYamagata, A. / Tainer, J.A.
CitationJournal: Embo J. / Year: 2007
Title: Hexameric structures of the archaeal secretion ATPase GspE and implications for a universal secretion mechanism.
Authors: Yamagata, A. / Tainer, J.A.
History
DepositionDec 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: 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_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.pdbx_leaving_atom_flag / _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
1: Type II secretion system protein
2: Type II secretion system protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,8285
Polymers119,7912
Non-polymers1,0373
Water00
1
1: Type II secretion system protein
2: Type II secretion system protein
hetero molecules

1: Type II secretion system protein
2: Type II secretion system protein
hetero molecules

1: Type II secretion system protein
2: Type II secretion system protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)362,48415
Polymers359,3736
Non-polymers3,1109
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Unit cell
Length a, b, c (Å)132.864, 132.864, 442.261
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
DetailsThe biological assembly is a hexamer generated from the dimer in the asymmetric unit by the operations: y-x,-x,z and -y,x-y,z

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Components

#1: Protein Type II secretion system protein / GspE-2


Mass: 59895.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: O29598
#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.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 3.13 Å3/Da / Density % sol: 60.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.9
Details: 10% PEG 8000, 5% PEG 400, 1.5 M NaCl, 0.1 M Na/K phosphate, pH 8.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.96333,0.97912,0.97802
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 4, 2004 / Details: mirros
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.963331
20.979121
30.978021
Reflection

D res low: 20 Å

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2D res high (Å)Num. obs% possible obs
1119.23038760.0911.373.127686100
1128.72773760.0971.453.225231100
10.937.72739650.1051.263.22521199.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.612099.710.0543.49810.4
5.276.6110010.0821.98510.8
4.625.2710010.0721.6611
4.24.6299.910.0671.23211.1
3.94.210010.0831.03211.1
3.673.910010.1060.94511.2
3.493.6710010.1410.89711.2
3.343.4910010.1990.86411.1
3.213.3410010.260.82611.1
3.13.2110010.340.78211
6.812099.820.0574.13110.4
5.446.8110020.0871.97410.7
4.775.4410020.0841.68411
4.334.7710020.0711.28211
4.034.3310020.0861.06211.1
3.794.0310020.1090.9811.2
3.63.7910020.1440.91911.2
3.453.610020.1810.86711.1
3.313.4510020.2620.84211.1
3.23.3110020.3340.79811.1
6.812099.930.0482.82510.4
5.446.8110030.0861.43210.7
4.775.4410030.0911.45911
4.334.7710030.0841.29911
4.034.3310030.1041.0911.1
3.794.0310030.133111.2
3.63.7910030.1760.92211.1
3.453.610030.2260.87311.1
3.313.4510030.3290.83811
3.23.3198.830.4310.78610
ReflectionResolution: 2.95→49.83 Å / Num. all: 32158 / Num. obs: 32158 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 10.9 % / Biso Wilson estimate: 118.8 Å2 / Limit h max: 39 / Limit h min: 0 / Limit k max: 39 / Limit k min: 0 / Limit l max: 149 / Limit l min: 0 / Observed criterion F max: 53079.17 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.106 / Χ2: 1.106 / Net I/σ(I): 7.2
Reflection shellResolution: 2.95→3.06 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 4.5 / Num. unique all: 3128 / Χ2: 0.622 / % possible all: 100

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 3.1 Å / D res low: 19.97 Å / FOM acentric: 0.606 / FOM centric: 0.448 / Reflection acentric: 24888 / Reflection centric: 2403
Phasing MAD set
IDHighest resolution (Å)Lowest resolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_13.119.9700248882398
ISO_23.119.971.3270.989226042220
ISO_33.119.970.4790.366225792218
ANO_13.119.972.0360248860
ANO_23.119.970.7660226020
ANO_33.119.971.1760224980
Phasing MAD set shell
IDResolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_111.48-19.9700353128
ISO_18.88-11.4800521116
ISO_17.51-8.8800670120
ISO_16.62-7.5100774103
ISO_15.98-6.6200894107
ISO_15.5-5.9800972108
ISO_15.12-5.5001054116
ISO_14.81-5.12001153100
ISO_14.55-4.81001206121
ISO_14.33-4.5500128393
ISO_14.14-4.33001346107
ISO_13.97-4.14001397110
ISO_13.82-3.97001470132
ISO_13.68-3.82001513141
ISO_13.56-3.68001610121
ISO_13.45-3.56001631136
ISO_13.35-3.45001697142
ISO_13.26-3.35001726125
ISO_13.18-3.26001785136
ISO_13.1-3.18001833136
ANO_111.48-19.974.03703530
ANO_18.88-11.484.9205210
ANO_17.51-8.885.32206700
ANO_16.62-7.515.11707740
ANO_15.98-6.624.69808940
ANO_15.5-5.984.05809720
ANO_15.12-5.53.69010540
ANO_14.81-5.123.502011530
ANO_14.55-4.813.257012060
ANO_14.33-4.553.052012830
ANO_14.14-4.332.559013460
ANO_13.97-4.142.056013970
ANO_13.82-3.971.807014700
ANO_13.68-3.821.555015130
ANO_13.56-3.681.381016100
ANO_13.45-3.561.157016310
ANO_13.35-3.451.012016970
ANO_13.26-3.350.876017260
ANO_13.18-3.260.787017850
ANO_13.1-3.180.726018310
ISO_211.48-19.973.0472.15353128
ISO_28.88-11.482.8221.92521116
ISO_27.51-8.882.9022.052670120
ISO_26.62-7.512.9842.28774103
ISO_25.98-6.622.6182.096894107
ISO_25.5-5.982.241.512972108
ISO_25.12-5.52.091.6491054116
ISO_24.81-5.121.9051.4871153100
ISO_24.55-4.811.6611.2481206121
ISO_24.33-4.551.6231.096128393
ISO_24.14-4.331.3230.81346107
ISO_23.97-4.141.2080.8831397110
ISO_23.82-3.971.0580.7041470132
ISO_23.68-3.820.9330.5981513141
ISO_23.56-3.680.8540.4371610121
ISO_23.45-3.560.7330.3951631136
ISO_23.35-3.450.6340.351697142
ISO_23.26-3.350.5470.3261726125
ISO_23.18-3.260.5120.309133494
ISO_23.1-3.180000
ANO_211.48-19.970.86103530
ANO_28.88-11.480.98805210
ANO_27.51-8.881.0706700
ANO_26.62-7.511.13807740
ANO_25.98-6.621.1808940
ANO_25.5-5.981.11509720
ANO_25.12-5.51.083010540
ANO_24.81-5.121.052011530
ANO_24.55-4.810.99012060
ANO_24.33-4.550.979012830
ANO_24.14-4.330.854013460
ANO_23.97-4.140.745013970
ANO_23.82-3.970.678014700
ANO_23.68-3.820.581015130
ANO_23.56-3.680.522016100
ANO_23.45-3.560.459016310
ANO_23.35-3.450.403016970
ANO_23.26-3.350.363017250
ANO_23.18-3.260.334013330
ANO_23.1-3.180000
ISO_311.48-19.970.6370.457353128
ISO_38.88-11.480.6420.434521116
ISO_37.51-8.880.6080.453670120
ISO_36.62-7.510.6660.503773102
ISO_35.98-6.620.6150.444894107
ISO_35.5-5.980.5880.398972108
ISO_35.12-5.50.5620.4121054116
ISO_34.81-5.120.5020.3831153100
ISO_34.55-4.810.4490.3581206121
ISO_34.33-4.550.4540.298128393
ISO_34.14-4.330.4290.3151346107
ISO_33.97-4.140.4330.3181397110
ISO_33.82-3.970.4190.2911470132
ISO_33.68-3.820.3950.31513141
ISO_33.56-3.680.3750.2311610121
ISO_33.45-3.560.3440.2181631136
ISO_33.35-3.450.3150.2011697142
ISO_33.26-3.350.2980.1961725125
ISO_33.18-3.260.2640.153131193
ISO_33.1-3.180000
ANO_311.48-19.972.83503530
ANO_38.88-11.483.31205210
ANO_37.51-8.883.91106700
ANO_36.62-7.513.23907730
ANO_35.98-6.622.91108940
ANO_35.5-5.982.32709720
ANO_35.12-5.52.053010540
ANO_34.81-5.121.996011530
ANO_34.55-4.811.712012060
ANO_34.33-4.551.677012830
ANO_34.14-4.331.321013460
ANO_33.97-4.141.062013970
ANO_33.82-3.970.928014700
ANO_33.68-3.820.773015130
ANO_33.56-3.680.682016100
ANO_33.45-3.560.59016300
ANO_33.35-3.450.516016920
ANO_33.26-3.350.46017220
ANO_33.18-3.260.413012390
ANO_33.1-3.180000
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1-27.733-79.25-419.029SE63.191.61
2-25.057-73.521-406.379SE63.781.29
3-15.461-51.206-424.124SE60.871.79
4-45.417-68.248-411.583SE39.871.2
5-20.471-97.44-429.187SE43.481.39
6-19.686-95.521-412.851SE79.771.66
7-32.914-111.892-416.439SE52.841.47
8-20.872-84.809-420.53SE58.471.41
9-23.616-108.333-418.481SE52.721.64
10-77.738-86.028-421.146SE71.991.65
11-58.431-67.98-418.351SE55.31.24
12-53.094-68.624-417.295SE49.461.24
13-84.461-79.929-434.214SE58.741.27
14-58.342-71.734-424.59SE58.221.39
15-87.781-74.144-430.781SE62.421.56
16-41.906-79.046-427.653SE49.241.15
17-39.116-97.668-396.935SE73.321.49
18-71.49-81.443-426.671SE57.421.45
19-72.318-86.477-421.584SE63.261.44
207.324-101.707-422.244SE49.031.33
21-5.876-99.546-425.296SE69.421.68
22-33.348-52.116-398.535SE68.621.48
2316.968-110.386-413.456SE49.861.51
24-107.085-40.264-430.041SE48.641.22
25-96.704-61.261-414.855SE96.541.63
26-40.391-92.588-390.333SE99.691.48
27-39.688-93.58-425.325SE84.651
28-23.459-83.538-397.662SE300.49
Phasing MAD shell
Resolution (Å)FOM acentricFOM centricReflection acentricReflection centric
11.48-19.970.9390.801353128
8.88-11.480.9170.753521118
7.51-8.880.9260.821670120
6.62-7.510.9110.682774105
5.98-6.620.880.702894107
5.5-5.980.8460.63972108
5.12-5.50.810.6531054116
4.81-5.120.8090.6121153100
4.55-4.810.7820.5241206122
4.33-4.550.7630.545128393
4.14-4.330.720.4911346107
3.97-4.140.6560.4331397110
3.82-3.970.5990.3421470132
3.68-3.820.5580.2271513141
3.56-3.680.5110.2171610121
3.45-3.560.460.2141631136
3.35-3.450.4160.1991697142
3.26-3.350.3720.1571726125
3.18-3.260.3250.141785136
3.1-3.180.2780.1511833136

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SOLOMONphasing
CNS1.1refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.95→49.83 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1542 4.8 %random
Rwork0.226 ---
all-32165 --
obs-31239 97.1 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 43.959 Å2 / ksol: 0.32981 e/Å3
Displacement parametersBiso max: 125.13 Å2 / Biso mean: 53.853 Å2 / Biso min: 11.27 Å2
Baniso -1Baniso -2Baniso -3
1-9.744 Å2-5.475 Å20 Å2
2--9.744 Å20 Å2
3----19.488 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.62 Å
Luzzati d res high-2.95
Refinement stepCycle: LAST / Resolution: 2.95→49.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7977 0 63 0 8040
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg23.1
X-RAY DIFFRACTIONx_torsion_impr_deg0.85
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.95-3.080.421945.30.40534470.033959364192
3.08-3.250.3191975.30.30735460.0233958374394.6
3.25-3.450.281854.80.26236320.0213971381796.1
3.45-3.720.2531884.80.22536960.0183992388497.3
3.72-4.090.1881995.10.18437300.0134000392998.2
4.09-4.680.1561874.70.16437860.0114013397399
4.68-5.90.1991994.90.19638500.0144067404999.6
5.9-49.830.2491934.60.24240100.0184222420399.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2anpB.paramanpB.top
X-RAY DIFFRACTION3ion.paramion.top

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