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- PDB-8j9c: Crystal structure of M61 peptidase (apo-form) from Xanthomonas ca... -

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Basic information

Entry
Database: PDB / ID: 8j9c
TitleCrystal structure of M61 peptidase (apo-form) from Xanthomonas campestris
ComponentsPutative glycyl aminopeptidase
KeywordsHYDROLASE / M61 peptidase / glycyl aminopeptidase / apo-form
Function / homology
Function and homology information


aminopeptidase activity
Similarity search - Function
Peptidase M61, catalytic domain / Peptidase M61 / Peptidase M61, N-terminal domain / M61 glycyl aminopeptidase / Peptidase M61 N-terminal domain / : / Tetratricopeptide TPR-3 / Tetratricopeptide repeat / Peptidase M4/M1, CTD superfamily / PDZ domain profile. ...Peptidase M61, catalytic domain / Peptidase M61 / Peptidase M61, N-terminal domain / M61 glycyl aminopeptidase / Peptidase M61 N-terminal domain / : / Tetratricopeptide TPR-3 / Tetratricopeptide repeat / Peptidase M4/M1, CTD superfamily / PDZ domain profile. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
Glycyl aminopeptidase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris B100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsYadav, P. / Kumar, A. / Jamdar, S.N. / Makde, R.D.
Funding support India, 1items
OrganizationGrant numberCountry
Other government India
CitationJournal: Febs J. / Year: 2024
Title: Crystal structure of a newly identified M61 family aminopeptidase with broad substrate specificity that is solely responsible for recycling acidic amino acids.
Authors: Jamdar, S.N. / Yadav, P. / Kulkarni, B.S. / Kumar, A. / Makde, R.D.
History
DepositionMay 3, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative glycyl aminopeptidase
B: Putative glycyl aminopeptidase
C: Putative glycyl aminopeptidase
D: Putative glycyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,90714
Polymers291,4394
Non-polymers46910
Water33,4721858
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, tetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.842, 94.512, 144.495
Angle α, β, γ (deg.)90.000, 104.170, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 22 through 31 or (resid 32...
d_2ens_1(chain "B" and (resid 22 through 31 or (resid 32...
d_3ens_1(chain "C" and (resid 22 through 49 or (resid 50...
d_4ens_1(chain "D" and (resid 22 through 31 or (resid 32...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALAALAALAAA22 - 12942 - 149
d_12SERSERMSEMSEAA131 - 179151 - 199
d_13THRTHRTRPTRPAA181 - 453201 - 473
d_14VALVALLEULEUAA455 - 479475 - 499
d_15SERSERARGARGAA481 - 626501 - 646
d_21ALAALAALAALABB22 - 12942 - 149
d_22SERSERMSEMSEBB131 - 179151 - 199
d_23THRTHRTRPTRPBB181 - 453201 - 473
d_24VALVALLEULEUBB455 - 479475 - 499
d_25SERSERARGARGBB481 - 626501 - 646
d_31ALAALAALAALACC22 - 12942 - 149
d_32SERSERMSEMSECC131 - 179151 - 199
d_33THRTHRTRPTRPCC181 - 453201 - 473
d_34VALVALLEULEUCC455 - 479475 - 499
d_35SERSERARGARGCC481 - 626501 - 646
d_41ALAALAALAALADD22 - 12942 - 149
d_42SERSERMSEMSEDD131 - 179151 - 199
d_43THRTHRTRPTRPDD181 - 453201 - 473
d_44VALVALLEULEUDD455 - 479475 - 499
d_45SERSERARGARGDD481 - 626501 - 646

NCS oper:
IDCodeMatrixVector
1given(-0.356934144133, 0.228052492449, -0.905864270981), (0.185737121857, -0.93305248422, -0.308082429318), (-0.915477874291, -0.278217760716, 0.290680476306)164.104374618, -16.1469807261, 111.488515814
2given(-0.739578983752, -0.672111701058, 0.035899694881), (-0.672820561716, 0.736801457713, -0.066604081286), (0.0183144348508, -0.0734130316265, -0.997133445565)162.913511511, 66.0314786642, 68.4578270347
3given(0.117726150337, 0.443990971386, 0.888263795758), (0.447586047568, -0.82219854376, 0.351647955577), (0.88645771673, 0.356176321457, -0.295518433408)55.4887392035, -64.3871391977, -37.6224261101

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Components

#1: Protein
Putative glycyl aminopeptidase


Mass: 72859.633 Da / Num. of mol.: 4 / Mutation: Q22A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris B100 (bacteria)
Gene: XCCB100_3176 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: B0RY21
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1858 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.37 Å3/Da / Density % sol: 48.19 % / Description: cuboid
Crystal growTemperature: 294 K / Method: batch mode / pH: 8.5 / Details: 0.1M Tris-Cl pH 8.5, 0.1M NaCl, 16% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97434 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 28, 2011 / Details: Mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97434 Å / Relative weight: 1
ReflectionResolution: 2.1→47.26 Å / Num. obs: 153445 / % possible obs: 96.3 % / Redundancy: 7.6 % / Biso Wilson estimate: 25.76 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.023 / Rrim(I) all: 0.064 / Net I/σ(I): 30.5
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 9.6 / Num. unique obs: 5614 / CC1/2: 0.99 / Rpim(I) all: 0.08 / Rrim(I) all: 0.217 / % possible all: 71.4

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RESOLVEmodel building
Cootmodel building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: SAD / Resolution: 2.1→47.26 Å / SU ML: 0.1813 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.6736
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1892 7680 5.01 %
Rwork0.1543 145702 -
obs0.1561 153382 96.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.5 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18936 0 15 1859 20810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002919492
X-RAY DIFFRACTIONf_angle_d0.596626507
X-RAY DIFFRACTIONf_chiral_restr0.04282822
X-RAY DIFFRACTIONf_plane_restr0.0053463
X-RAY DIFFRACTIONf_dihedral_angle_d5.42892656
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.471171909695
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.384589295387
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.404118145702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.21281790.17943502X-RAY DIFFRACTION70.21
2.12-2.150.27272210.17593759X-RAY DIFFRACTION74.76
2.15-2.180.21131940.17184239X-RAY DIFFRACTION82.98
2.18-2.20.23382380.17834634X-RAY DIFFRACTION92.69
2.2-2.230.23982710.16644899X-RAY DIFFRACTION97.99
2.23-2.260.22662360.17034935X-RAY DIFFRACTION97.92
2.26-2.290.20642610.16874918X-RAY DIFFRACTION98.16
2.29-2.330.20862710.16514956X-RAY DIFFRACTION98.14
2.33-2.370.21872560.17264970X-RAY DIFFRACTION98.21
2.37-2.40.21672780.17134907X-RAY DIFFRACTION98.26
2.4-2.450.19812400.17514934X-RAY DIFFRACTION98.29
2.45-2.490.2072660.17574969X-RAY DIFFRACTION98.42
2.49-2.540.23722570.17464945X-RAY DIFFRACTION98.41
2.54-2.590.23042320.16814985X-RAY DIFFRACTION98.42
2.59-2.650.19652820.16124942X-RAY DIFFRACTION98.57
2.65-2.710.20682650.1724986X-RAY DIFFRACTION98.7
2.71-2.780.20412980.17214949X-RAY DIFFRACTION98.76
2.78-2.850.22232490.16894967X-RAY DIFFRACTION98.68
2.85-2.930.20963020.17174945X-RAY DIFFRACTION98.79
2.93-3.030.23852670.1774979X-RAY DIFFRACTION98.85
3.03-3.140.21622640.17625014X-RAY DIFFRACTION98.78
3.14-3.260.20562570.1715003X-RAY DIFFRACTION98.97
3.26-3.410.1882830.1554957X-RAY DIFFRACTION99.02
3.41-3.590.16352580.1495031X-RAY DIFFRACTION98.92
3.59-3.820.17842300.14495052X-RAY DIFFRACTION98.99
3.82-4.110.16412610.13285027X-RAY DIFFRACTION98.97
4.11-4.520.13832690.11995023X-RAY DIFFRACTION99.12
4.52-5.180.14262620.11675056X-RAY DIFFRACTION99.11
5.18-6.520.16552560.13555099X-RAY DIFFRACTION99.41
6.52-47.260.16212770.14935120X-RAY DIFFRACTION98.09
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)
10.5211218244220.0394009023817-0.03675910348130.4833841644860.1423558648010.2294591107560.0598511716209-0.169928389037-0.06971631916350.0801463103832-0.09041206529580.0680135462080.0387883942244-0.02762780395090.02873432941030.196279243976-0.04492392790870.00310320628560.2615455427750.04581656338410.169138627752120.288316111-11.945872302965.7129422346
20.395265987772-0.1754162988-0.1932651871981.12642607666-0.03457831409931.223472660960.0233259445176-0.0606569562085-0.08490142922640.0203782160955-0.01094417901520.03369398404330.00152899192305-0.0375275263819-0.01438689935010.159123150085-0.03454978730140.004659728583510.237381179190.04395385030620.191373869745137.198305771-18.053925065249.5090052402
31.40347244857-1.073369622120.7711044786851.48187196024-0.5679820148830.7580189892230.132183550490.243905785617-0.177806346916-0.203228812604-0.1325553058580.1703029143130.134294336869-0.0389831289107-0.006358810214760.176857614301-0.0102865707392-0.0143160988550.276377128405-0.03095851005490.172398663351122.111820805-13.051024332328.2716993062
40.5507458596740.0577994919978-0.07902199309370.473982907816-0.009271395563510.5851225992430.04040260798830.07585953030740.05200606581290.0123472577058-0.0354948981775-0.0290524923808-0.0208814008061-0.0818064416181-0.005799157402650.165766576455-0.01324692675510.005683366941240.2249022848520.01287527326650.2016856949459.0123462002-2.8496484720823.7913477585
52.53436451417-0.512111389742-0.1370160267250.6305788201230.08228507129410.7882806544110.05886071483560.2088911946710.205307471735-0.0305088048598-0.05715538425180.025646243101-0.202295440063-0.00895486034314-0.007562127739750.252963310079-0.003245091717120.01886483868660.2830534698130.06898101927120.20422972637567.22420329110.90050966095.55553560037
61.53826900712-0.3286653143360.3011437226680.590694120350.05603829071780.773662008897-0.01100279572110.3370385557480.294959096330.05235492007310.0115886999955-0.154721862764-0.2014086700670.3118110254340.00734824238520.222916305129-0.0774065634497-0.00227756312630.3260040353160.06407384447430.22216381657891.88736121659.8993167397411.7746798908
72.683788239250.9878670607421.901391440921.748424542631.446555424993.55708701872-0.03658416558180.495407742041-0.199366467532-0.1647388484520.04995222370510.05562358585850.1396751766870.117613839293-0.02241827528710.2433791332480.02830316607910.002240805142440.334277355511-0.05010319015930.19975472659179.1981792947-18.1560884033-7.27326838007
80.4857846764140.119896318363-0.1142018544740.490755259565-0.08914952651530.98585922710.01290785346670.087804127283-0.22488299862-0.0127302777887-0.0101446379026-0.07795480609560.2648510557030.157089125111-7.89432946987E-60.2975654186880.0534764041619-0.01671264779760.287741050423-0.06821366492160.29579801706984.9753341656-29.34255653257.69299906161
90.988490065589-0.562808560068-0.1182846923070.6115821252720.8132277900271.913320711920.1122542313770.0157166420348-0.448699753489-0.05325666832450.001178537796850.05696104693230.480775999358-0.0111365447318-0.1048397015480.468826191239-0.0418928862266-0.04519078021370.227068667734-0.004589547014950.4334451318472.8726594451-44.162138052818.0903094872
104.00979433836-0.7854257300172.04845479170.6080737618190.2397491164861.957413812030.0947898983438-0.0265640194481-0.3435856565860.1083701015190.09397921729690.08680825751650.3457146546550.150699571229-0.1972183396910.5438702347530.0185769037631-0.04268812237370.2667241737790.09403979662810.4387819696980.8116753499-41.64332340935.6606461132
113.77777602311.787755941012.586743067286.37346487005-1.096559414125.80715672687-0.04718277400730.265457109212-0.325042377033-0.2972866404960.0316279785609-0.3676921931550.3076600327260.2546693388510.02365131960120.184869304084-0.000996502065412-0.02597319968450.178084204966-0.01836680101550.22438599336580.9421285705-22.430481779540.090237842
120.644251216495-0.100162609345-0.1388623188210.9869772143920.5494416131950.8206346650760.0861926670435-0.196470869517-0.230831344250.10472161929-0.0822825488037-0.05252271289540.4167448257720.1155143564870.02225880811820.3477030215120.0172505720948-0.09558426626980.2315736168990.05855047607380.36025285538284.0465806525-30.178830041444.5719949288
130.6731672675830.0535782143163-0.05446411814830.6095147576990.1500876318640.591752154589-0.02677295801240.05751864454360.173217187823-0.0166977949963-0.029262541290.111036564737-0.1362244254390.02702341706390.05657189170160.22070647386-0.0263117540293-0.01330803775850.1796470475620.01031571696750.209807375826123.46551583522.749448614844.0781716381
141.034914790240.3060094729730.03750662021050.655164674917-0.2628392982560.7189737758650.0287203690732-0.2323268487270.3656061828280.0872860707942-0.06839476382240.192168226027-0.226597932073-0.04370823129690.04318827289730.268935124491-0.015315279370.02572385904920.242056444005-0.1074620936120.334362894228108.50922229727.713194871364.1285687453
155.71983811251-0.5073546620661.521670761083.604168988152.751081873123.53232402574-0.03458400729210.1385018739970.194306751466-0.3542604981710.02516338879450.12014770109-0.3164808111720.06852459244380.01025521035620.203921166971-0.0423420801428-0.007149568575160.218812399028-0.03369550841880.27520443845293.84846752036.9783845727255.9970677474
161.109668850040.4286322287520.1564943959362.21736435270.1018387396660.7124124686540.0758663053631-0.1152836891270.2823922628780.1372479023390.006607508464130.225963455852-0.0516777694071-0.151832865102-0.06264767037990.1721908292320.010716943116-6.85477483122E-50.236958027928-0.06038518785650.31406522496787.183178986213.317585774557.0742110973
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 22 through 397 )AA22 - 3971 - 376
22chain 'A' and (resid 398 through 519 )AA398 - 519377 - 498
33chain 'A' and (resid 520 through 626 )AA520 - 626499 - 605
44chain 'B' and (resid 22 through 397 )BC22 - 3971 - 376
55chain 'B' and (resid 398 through 527 )BC398 - 527377 - 506
66chain 'B' and (resid 528 through 626 )BC528 - 626507 - 605
77chain 'C' and (resid 22 through 66 )CD22 - 661 - 45
88chain 'C' and (resid 67 through 397 )CD67 - 39746 - 376
99chain 'C' and (resid 398 through 483 )CD398 - 483377 - 462
1010chain 'C' and (resid 484 through 513 )CD484 - 513463 - 492
1111chain 'C' and (resid 514 through 554 )CD514 - 554493 - 533
1212chain 'C' and (resid 555 through 626 )CD555 - 626534 - 605
1313chain 'D' and (resid 22 through 376 )DE22 - 3761 - 355
1414chain 'D' and (resid 377 through 513 )DE377 - 513356 - 492
1515chain 'D' and (resid 514 through 554 )DE514 - 554493 - 533
1616chain 'D' and (resid 555 through 626 )DE555 - 626534 - 605

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Yorodumi

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  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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