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- PDB-3ivl: The Crystal Structure of the Inactive Peptidase Domain of a Putat... -

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Basic information

Entry
Database: PDB / ID: 3ivl
TitleThe Crystal Structure of the Inactive Peptidase Domain of a Putative Zinc Protease from Bordetella parapertussis to 2.2A
ComponentsPutative zinc protease
KeywordsHYDROLASE / protease / inactive / peptidase / bordetella / parapertussis / PSI / MCSG / Structural Genomics / Midwest Center for Structural Genomics / Protein Structure Initiative
Function / homology
Function and homology information


metalloendopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
: / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like ...: / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Zinc protease
Similarity search - Component
Biological speciesBordetella parapertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsStein, A.J. / Wu, R. / Keigher, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The Crystal Structure of the Inactive Peptidase Domain of a Putative Zinc Protease from Bordetella parapertussis to 2.2A
Authors: Stein, A.J. / Wu, R. / Keigher, L. / Joachimiak, A.
History
DepositionSep 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Putative zinc protease
B: Putative zinc protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0734
Polymers45,8612
Non-polymers2122
Water91951
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative zinc protease
hetero molecules

A: Putative zinc protease
hetero molecules

A: Putative zinc protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1096
Polymers68,7913
Non-polymers3183
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 area4740 Å2
ΔGint-17 kcal/mol
Surface area27610 Å2
MethodPISA
3
B: Putative zinc protease
hetero molecules

B: Putative zinc protease
hetero molecules

B: Putative zinc protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1096
Polymers68,7913
Non-polymers3183
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area3960 Å2
ΔGint-30 kcal/mol
Surface area27050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.173, 108.173, 113.995
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Detailsauthors state that biological unit is the same as asymmetric unit.

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Components

#1: Protein Putative zinc protease


Mass: 22930.289 Da / Num. of mol.: 2 / Fragment: residues 258-465, Inactive Peptidase Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella parapertussis (bacteria) / Gene: BPP3483 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7W521
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 6.5
Details: 40% PEG 300, 0.1M Sodium cacodylate pH 6.5, 0.2M Calcium acetate, vapor diffusion, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 14, 2009
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 28929 / % possible obs: 99.6 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.099 / Χ2: 2.809 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.184.40.7228961.1311100
2.18-2.264.40.47929131.2941100
2.26-2.374.40.43228981.2091100
2.37-2.494.40.26929141.3371100
2.49-2.654.40.19528881.4081100
2.65-2.854.40.13429121.6791100
2.85-3.144.40.09828982.219199.9
3.14-3.594.40.0829053.5781100
3.59-4.524.30.0729095.623199.8
4.52-504.30.0727969.141196.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.5.0102refinement
PDB_EXTRACT3.004data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXphasing
MLPHAREphasing
DMphasing
ARP/wARPmodel building
Cootmodel building
RefinementResolution: 2.2→43.33 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.253 / WRfactor Rwork: 0.213 / SU B: 14.902 / SU ML: 0.168 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1273 5.1 %RANDOM
Rwork0.216 ---
obs0.219 25100 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0.03 Å20 Å2
2---0.07 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.2→43.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2752 0 14 51 2817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222833
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.9813863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6285371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.86522.477109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.87715419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6791525
X-RAY DIFFRACTIONr_chiral_restr0.0980.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212151
X-RAY DIFFRACTIONr_mcbond_it0.5181.51850
X-RAY DIFFRACTIONr_mcangle_it0.93622934
X-RAY DIFFRACTIONr_scbond_it1.843983
X-RAY DIFFRACTIONr_scangle_it2.7124.5927
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.201-2.2580.333980.3281738183799.946
2.258-2.320.325920.2971720181399.945
2.32-2.3870.321110.27416751786100
2.387-2.460.263820.24616441726100
2.46-2.540.3251020.2515541656100
2.54-2.6290.245730.2431519159399.937
2.629-2.7280.333690.24215041573100
2.728-2.8390.253660.22714231489100
2.839-2.9650.227790.2291353143399.93
2.965-3.1090.279590.2261282134299.925
3.109-3.2760.242760.21312571333100
3.276-3.4730.23610.2091157121999.918
3.473-3.7110.291430.21611181161100
3.711-4.0060.245680.1871010107999.907
4.006-4.3850.24500.18192397799.591
4.385-4.8960.234340.16287491599.235
4.896-5.6420.207440.19875180199.251
5.642-6.8810.199240.22363065899.392
6.881-9.610.218300.18246952395.411
9.61-43.3250.462120.26622630578.033
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)
11.4217-3.1434-2.85057.81276.60295.9411-0.0946-0.06010.0451-0.11480.2532-0.3363-0.0290.1344-0.15860.203-0.01630.02540.1446-0.04410.25649.143430.71751.4669
22.55953.5016-2.894523.908819.843433.4966-0.03030.4278-0.0595-0.50110.0191-0.0661-0.38-1.0480.01120.16860.01990.10790.17220.0290.318719.20979.743-10.1681
342.961827.1848.478721.685415.67125.44740.5117-0.2211-1.98660.78770.0575-1.35281.33670.3274-0.56920.5072-0.00540.00490.2041-0.03720.388821.3781-3.7361-10.4544
413.9281-1.5912-3.888715.10813.88471.9956-0.1749-0.21480.20480.14890.1876-0.03350.0793-0.0647-0.01280.2104-0.0332-0.07290.2478-0.00330.118321.08813.18020.1398
59.9746-5.3623-2.895112.776311.103710.2755-0.1189-1.44620.1220.3720.4235-0.5039-0.03850.1113-0.30450.6627-0.1283-0.24630.3773-0.10650.526921.844117.58417.9397
69.6557-7.4728-8.660116.087911.185610.85860.1504-0.61120.29030.2673-0.0659-0.381-0.28790.2757-0.08450.3534-0.06160.00060.2291-0.040.162214.567212.46321.2089
720.63545.91939.99235.41493.60325.05230.2074-0.8195-0.1366-0.603-0.34951.15190.0559-0.49270.14210.5436-0.20560.02560.4177-0.07910.574712.91024.9464-9.9368
810.8965-10.9141-2.241145.049410.72793.04430.4758-0.14061.32410.8109-0.3017-1.11520.074-0.1903-0.1740.28390.00020.02240.2223-0.06620.276814.731421.76321.8868
954.8689-2.264-8.415120.77174.22422.05720.4143-0.52291.0420.3517-0.029-1.2443-0.05450.1118-0.38530.55630.01830.23790.1097-0.12260.798719.205228.6614-1.2979
1010.3712-5.3524-1.24773.6756-0.15662.48070.19880.042-0.21720.1431-0.1453-0.5844-0.13330.4002-0.05350.3685-0.1541-0.10370.2682-0.09080.888627.666715.8134-2.4534
1118.87460.5164-6.967111.1971-3.924113.2163-0.3812-1.79390.64031.33660.2316-1.3819-0.23511.1170.14950.30080.0239-0.21250.4517-0.19210.350227.87491.4527.4194
1212.75137.67193.44319.37150.41774.31520.2861-1.05920.04720.8196-0.39530.5164-0.4921-0.42270.10920.54410.14640.08960.16720.0170.095913.5947-6.11495.8186
136.9601-1.82773.30179.21282.092431.0664-0.0527-0.4655-0.2359-0.4287-0.22021.2949-0.9528-1.07260.27290.18250.0255-0.02580.2049-0.02710.4283.8269-8.879-3.6539
1412.69055.30687.36176.18614.02054.6745-0.13060.6358-0.3819-0.09930.1707-0.179-0.17270.264-0.04010.20160.031-0.00140.1794-0.02250.207217.2903-11.5258-3.4079
152.0868-2.19822.62375.544-4.85557.14810.436-0.11680.2315-0.7965-0.3072-1.07610.44860.2322-0.12880.2447-0.02910.21690.21770.03880.629628.66295.0848-6.9847
1620.4083-9.9771-7.64756.35713.60518.50020.10770.48711.8945-0.2809-0.2788-1.1822-0.8324-0.60290.17110.30280.04570.00710.1111-0.04230.399412.789323.8942-7.6925
170.71112.11793.811247.917721.757526.3198-0.0360.2868-0.22-1.9218-0.0641.5021-0.21041.03480.10010.42010.17640.10640.3611-0.03240.50690.507842.15010.1363
188.4173-1.49626.45490.3785-1.22786.1422-0.05530.5523-0.03510.0892-0.1519-0.1908-0.03110.86030.20720.2507-0.0091-0.10320.22470.08070.389275.34946.9292-17.8516
196.5878-7.5070.118211.1113-0.21035.8279-0.00510.19750.25480.2858-0.04610.3042-0.5675-0.35230.05120.17240.0060.02860.19690.08520.163344.063313.4089-27.8989
209.1355-3.46564.12419.55110.11572.40050.2525-0.2366-0.01630.7887-0.11330.07540.0655-0.0781-0.13920.45310.03310.20970.32850.04050.135145.557911.2464-17.6395
216.6011-1.94276.779912.1965-4.36797.6384-0.1406-1.65820.52510.9759-0.24160.4345-0.5288-1.50910.38220.69120.02620.06560.6019-0.04680.237752.55056.9276-10.1692
222.8867-2.11263.001413.7658-1.96547.96330.0577-0.5112-0.07980.8498-0.0202-0.27020.18380.4866-0.03750.3937-0.0068-0.03470.36130.07870.058260.11674.138-12.6079
236.10743.42911.25959.4144-4.114110.040.01340.25050.5730.3143-0.0686-0.0466-0.8677-0.13950.05530.26830.07290.03360.2252-0.02070.18950.989517.9341-27.0887
2420.06216.71114.01633.38190.7662.47560.14220.0133-0.82960.24140.0255-0.52440.00240.4009-0.16770.31980.0095-0.11170.20570.04040.197963.57117.726-17.7082
2553.12214.745713.147510.2594-2.42459.4697-0.28211.9177-3.21550.21740.608-1.5111-0.22820.6166-0.3260.30160.0878-0.0260.272-0.21510.582267.0218-0.473-20.1891
2635.84714.47113.237925.7895-3.85778.8418-0.3061-0.207-1.2399-0.10040.33020.4752-0.32830.0144-0.02420.35690.02890.03090.19540.01930.06657.36290.2994-21.5238
2717.19383.0586-6.11563.0385-2.4834.9427-0.32750.0696-0.90280.37050.29960.45520.5454-0.26140.02790.31280.04650.12510.13250.07820.383846.1307-0.7527-19.8268
281.1547-2.3703-3.560513.48668.57412.7813-0.1159-0.2532-0.37891.0406-0.68550.56520.4955-0.29720.80130.36250.02090.11830.77220.33030.256239.9178.3296-10.4268
290.13990.5474-0.063418.6322-2.67680.4141-0.029-0.22480.03051.31740.060.3263-0.1154-0.0422-0.0310.37510.11440.05640.4304-0.00440.104240.818422.8493-12.819
306.8654-1.2171.45913.165-0.445515.6687-0.0183-0.13110.32120.37140.0643-0.49790.21451.0305-0.04610.23350.06670.01030.2240.00690.251343.212832.4566-22.2025
316.2015-1.6494-0.625410.0214-4.86285.7564-0.3098-0.2179-0.0822-0.49040.10280.2390.5120.27920.20710.17780.04930.03910.18270.00480.23735.35425.8543-22.9699
326.4295-2.0812-4.43650.99961.98726.5241-0.23480.334-0.17810.2778-0.02690.3360.153-0.45760.26170.24830.05250.1320.19020.0660.433637.76638.5737-21.6731
331.01531.5394-0.84776.34021.12332.50160.14850.0141-0.17420.3036-0.1079-0.3872-0.08810.1444-0.04060.18950.01930.00130.2035-0.01630.124559.33424.8511-29.2555
3424.9681-1.611212.4430.3528-0.74766.3858-0.03321.35510.0394-0.2237-0.02450.3106-0.12410.37940.05760.32730.0492-0.13160.63270.15250.592385.21286.6714-20.3477
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A270 - 282
2X-RAY DIFFRACTION2A283 - 287
3X-RAY DIFFRACTION3A288 - 294
4X-RAY DIFFRACTION4A295 - 307
5X-RAY DIFFRACTION5A308 - 323
6X-RAY DIFFRACTION6A324 - 330
7X-RAY DIFFRACTION7A331 - 340
8X-RAY DIFFRACTION8A341 - 347
9X-RAY DIFFRACTION9A348 - 353
10X-RAY DIFFRACTION10A354 - 368
11X-RAY DIFFRACTION11A369 - 377
12X-RAY DIFFRACTION12A378 - 390
13X-RAY DIFFRACTION13A391 - 406
14X-RAY DIFFRACTION14A407 - 423
15X-RAY DIFFRACTION15A424 - 439
16X-RAY DIFFRACTION16A440 - 449
17X-RAY DIFFRACTION17A450 - 456
18X-RAY DIFFRACTION18B270 - 282
19X-RAY DIFFRACTION19B283 - 297
20X-RAY DIFFRACTION20B298 - 306
21X-RAY DIFFRACTION21B307 - 314
22X-RAY DIFFRACTION22B315 - 328
23X-RAY DIFFRACTION23B329 - 340
24X-RAY DIFFRACTION24B341 - 347
25X-RAY DIFFRACTION25B348 - 353
26X-RAY DIFFRACTION26B354 - 360
27X-RAY DIFFRACTION27B361 - 369
28X-RAY DIFFRACTION28B370 - 378
29X-RAY DIFFRACTION29B379 - 389
30X-RAY DIFFRACTION30B390 - 408
31X-RAY DIFFRACTION31B409 - 418
32X-RAY DIFFRACTION32B419 - 436
33X-RAY DIFFRACTION33B437 - 446
34X-RAY DIFFRACTION34B447 - 456

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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