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- PDB-2gre: Crystal structure of Deblocking aminopeptidase from Bacillus cereus -

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Basic information

Entry
Database: PDB / ID: 2gre
TitleCrystal structure of Deblocking aminopeptidase from Bacillus cereus
ComponentsDeblocking aminopeptidase
KeywordsHYDROLASE / Bacillus cereus Deblocking aminopeptidase / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / aminopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase M42, domain 2 / Peptidase M42, domain 2 / : / M42 glutamyl aminopeptidase / Peptidase M42 / Zn peptidases / Elongation Factor Tu (Ef-tu); domain 3 / Aminopeptidase / Beta Barrel / 3-Layer(aba) Sandwich ...Peptidase M42, domain 2 / Peptidase M42, domain 2 / : / M42 glutamyl aminopeptidase / Peptidase M42 / Zn peptidases / Elongation Factor Tu (Ef-tu); domain 3 / Aminopeptidase / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Deblocking aminopeptidase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsChang, C. / Wu, R. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of Deblocking aminopeptidase from Bacillus cereus
Authors: Chang, C. / Wu, R. / Abdullah, J. / Joachimiak, A.
History
DepositionApr 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 6, 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_ref_seq_dif / 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_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: Deblocking aminopeptidase
B: Deblocking aminopeptidase
C: Deblocking aminopeptidase
D: Deblocking aminopeptidase
E: Deblocking aminopeptidase
F: Deblocking aminopeptidase
G: Deblocking aminopeptidase
H: Deblocking aminopeptidase
I: Deblocking aminopeptidase
J: Deblocking aminopeptidase
K: Deblocking aminopeptidase
L: Deblocking aminopeptidase
M: Deblocking aminopeptidase
N: Deblocking aminopeptidase
O: Deblocking aminopeptidase
P: Deblocking aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)629,35932
Polymers627,82216
Non-polymers1,53716
Water17,691982
1
A: Deblocking aminopeptidase
B: Deblocking aminopeptidase
C: Deblocking aminopeptidase
D: Deblocking aminopeptidase
E: Deblocking aminopeptidase
F: Deblocking aminopeptidase
G: Deblocking aminopeptidase
H: Deblocking aminopeptidase
I: Deblocking aminopeptidase
J: Deblocking aminopeptidase
K: Deblocking aminopeptidase
L: Deblocking aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)472,01924
Polymers470,86712
Non-polymers1,15312
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
M: Deblocking aminopeptidase
N: Deblocking aminopeptidase
O: Deblocking aminopeptidase
P: Deblocking aminopeptidase
hetero molecules

M: Deblocking aminopeptidase
N: Deblocking aminopeptidase
O: Deblocking aminopeptidase
P: Deblocking aminopeptidase
hetero molecules

M: Deblocking aminopeptidase
N: Deblocking aminopeptidase
O: Deblocking aminopeptidase
P: Deblocking aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)472,01924
Polymers470,86712
Non-polymers1,15312
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)240.918, 240.918, 294.824
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Deblocking aminopeptidase


Mass: 39238.875 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Plasmid: pMCSG / Production host: Escherichia coli (E. coli)
References: GenBank: 29894598, UniProt: Q81HB5*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 982 / 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: 2.62 Å3/Da / Density % sol: 53.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2.0 M Ammonium sulfate, Na-cacodylate pH6.5, NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 26, 2006
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 206788 / Num. obs: 206788 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 2.64
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.756 / Mean I/σ(I) obs: 2.52 / Num. unique all: 20704 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data scaling
HKL-3000phasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.65→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.898 / SU B: 25.573 / SU ML: 0.263 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.788 / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26394 9285 5 %RANDOM
Rwork0.19439 ---
all0.19789 175594 --
obs0.19789 175594 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.235 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.09 Å20 Å2
2--0.17 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38497 0 80 982 39559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02239170
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8611.95952963
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.79454833
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.57724.4971739
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.846156885
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.57915192
X-RAY DIFFRACTIONr_chiral_restr0.1330.26125
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0228842
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2660.220071
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3230.226488
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2250.22096
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.2134
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.230.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1161.524892
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.646239244
X-RAY DIFFRACTIONr_scbond_it2.369315974
X-RAY DIFFRACTIONr_scangle_it3.6634.513719
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 713 -
Rwork0.276 12887 -
obs--99.37 %
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)
11.6185-0.11280.07971.13790.71672.4215-0.17120.02750.02210.0420.0121-0.062-0.16670.05520.1592-0.3063-0.0192-0.0778-0.38150.0464-0.3981106.697732.839104.5369
27.2421.2310.41974.85870.77759.67530.1038-0.5436-0.60260.21240.0611-0.240.60.1002-0.1649-0.263-0.0187-0.0816-0.28970.0854-0.3709113.609828.82135.1212
31.16780.15790.62822.7516-0.00761.3665-0.0222-0.0331-0.10270.13120.03370.2217-0.01380.102-0.0115-0.3240.06770.0423-0.45130.0358-0.392985.109115.5747133.0011
43.79740.30330.60498.6017-0.53356.93940.08440.2633-0.0732-0.5893-0.056-0.61530.35960.4424-0.0284-0.23930.09220.035-0.3863-0.0149-0.339391.7747-14.5692126.507
51.58350.0828-0.67541.5711-0.55651.388-0.01560.3349-0.00760.0264-0.0085-0.08350.0619-0.04620.0241-0.38110.0097-0.0042-0.298-0.0581-0.316989.2015-2.260797.7231
67.86111.0207-2.42316.8919-0.52896.43560.0311-0.58260.27720.28010.0265-0.54070.01970.3489-0.0576-0.4175-0.009-0.0083-0.275-0.054-0.2535118.74637.088491.1513
70.59430.8031-0.40042.9819-0.2491.2694-0.13660.2821-0.1008-0.01850.0953-0.57340.06080.30050.0413-0.29020.0707-0.0108-0.0445-0.18860.1805166.2652-28.1397103.2975
85.5505-0.27952.37677.0512-0.42455.923-0.0014-0.0141-0.13470.06010.06590.6478-0.2212-0.1483-0.0646-0.3028-0.0849-0.0212-0.2003-0.1286-0.0516154.4820.985397.6832
91.98210.7225-0.07173.05440.17251.3304-0.10540.3565-0.1937-0.29890.1789-0.32930.01310.1914-0.0735-0.2759-0.02720.1243-0.0819-0.1922-0.1556136.6274-16.786678.8618
107.5871-0.4-1.22577.3227-1.16833.7922-0.2086-0.8107-0.2050.46630.0808-0.12560.010.41850.1277-0.32420.06980.0979-0.3367-0.1138-0.2971112.231-24.447297.6035
111.9365-0.44860.65671.5501-0.16282.1784-0.0743-0.2250.01770.18450.0862-0.04330.17420.0574-0.0119-0.24950.04160.0587-0.3884-0.1671-0.2612131.949-48.2246102.6533
126.59490.909-0.63252.74630.4915.5451-0.2541-0.29220.15490.19460.10860.0065-0.87140.01410.1455-0.04720.1426-0.052-0.2216-0.0856-0.1872148.9722-37.8281127.3072
131.81730.1678-0.36271.2311-0.38133.16420.0543-0.28150.12010.2679-0.128-0.1662-0.38840.2780.0737-0.0915-0.1941-0.1539-0.16430.0245-0.2446143.036239.2776142.6159
146.6851.10530.19433.25630.69229.19560.14460.2714-0.66110.09230.0685-0.12910.61120.3643-0.2132-0.3509-0.0977-0.0716-0.27430.0183-0.2632137.508529.9102112.8793
151.7248-0.71770.35032.24990.12831.0565-0.00980.052-0.2385-0.05110.0776-0.11760.088-0.0019-0.0677-0.3386-0.1636-0.0142-0.27770.0379-0.2492168.266323.7127116.0646
163.9506-0.90781.44367.86-0.75936.80740.0117-0.0742-0.51960.5042-0.02130.73880.2668-0.14950.0095-0.3458-0.0655-0.058-0.2480.0487-0.0158167.6468-6.2774126.6222
172.20350.4682-1.49031.26160.24041.9173-0.0136-0.4422-0.11630.2713-0.0135-0.1592-0.16140.3630.027-0.1769-0.0901-0.17220.07820.1905-0.1039167.82719.8022153.5403
185.97370.5805-1.66066.1547-2.41216.2247-0.06230.63770.1548-0.17840.09560.36870.0094-0.1842-0.0333-0.1687-0.0741-0.0316-0.12480.1551-0.232136.648613.6148159.3432
190.9778-0.39480.07353.43490.47512.6311-0.1038-0.1366-0.23110.3535-0.02420.14350.4203-0.01190.1280.00570.05690.1283-0.33250.1046-0.25197.6162-31.9523153.163
203.63910.4190.84787.82-0.21816.1293-0.07620.39820.13830.0015-0.0868-0.9176-0.16030.47190.163-0.19670.03410.0131-0.33780.094-0.4214103.0615-0.6754153.9407
212.6027-0.22830.10931.151-0.18811.08930.07230.0009-0.0037-0.0151-0.142-0.1769-0.06540.27660.0697-0.11440.020.0354-0.25150.0873-0.4459123.8446-11.4536175.0967
227.9862-0.2936-1.75716.04811.03593.5591-0.15270.9468-0.0187-0.28240.0305-0.19450.1283-0.12520.1222-0.1840.06420.01260.00890.1513-0.3287149.4947-16.2941156.914
231.2510.66470.47361.30620.63932.23480.0502-0.0073-0.31960.1793-0.06010.04040.4650.25680.00990.1170.26260.0228-0.10930.1069-0.1658135.5271-44.1499155.7272
248.0704-0.81160.08064.37033.04787.7587-0.31750.22870.21590.07990.14090.1256-0.4991-0.42530.1766-0.07440.12340.0508-0.2238-0.0336-0.2471116.8082-41.2647130.045
251.99960.5733-0.59342.96060.21152.2941-0.07970.2631-0.2855-0.160.1611-0.4520.08150.2911-0.0815-0.13530.04030.09760.0834-0.2040.103145.399-18.803116.1121
265.39050.1338-1.89277.84170.44077.32890.27140.29120.1038-0.3967-0.14010.3648-0.3975-0.4613-0.1313-0.19880.01550.097-0.0641-0.0326-0.152734.59989.207126.2586
270.8707-0.6532-0.64772.97130.26562.0985-0.06250.05910.06540.05430.1548-0.09820.13550.1537-0.0923-0.1948-0.0087-0.0099-0.139-0.1031-0.214921.78287.6653155.6245
287.98890.0359-1.385410.34690.58486.3172-0.08550.5279-0.1815-0.3643-0.05110.38610.2812-0.46030.1366-0.1245-0.04130.0211-0.0932-0.1233-0.173721.669-18.6209138.0116
293.0356-0.0930.92691.88980.1060.69560.13670.33450.4287-0.1688-0.0102-0.0796-0.28670.281-0.12640.20040.13790.12590.35040.22670.0608-1.466736.189878.7217
308.2807-0.3241-0.28715.0491.64837.45-0.0872-0.564-0.09650.32020.2682-0.0058-0.1096-0.3261-0.181-0.03960.11720.12460.11730.07750.049317.867333.3361103.7567
311.772-0.25990.3440.9601-0.38492.65330.02340.29880.1797-0.0416-0.05950.0771-0.0394-0.21710.0361-0.214-0.04740.1185-0.0248-0.0386-0.024944.342816.172197.3032
324.9149-0.28791.88615.90091.14637.13350.1702-0.1842-0.3955-0.24940.08390.43940.102-0.7513-0.2541-0.0861-0.00830.06610.28810.03880.010718.228911.015179.8258
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 734 - 73
2X-RAY DIFFRACTION1AA168 - 348168 - 348
3X-RAY DIFFRACTION2AA74 - 16774 - 167
4X-RAY DIFFRACTION3BB4 - 734 - 73
5X-RAY DIFFRACTION3BB168 - 348168 - 348
6X-RAY DIFFRACTION4BB74 - 16774 - 167
7X-RAY DIFFRACTION5CC4 - 734 - 73
8X-RAY DIFFRACTION5CC168 - 348168 - 348
9X-RAY DIFFRACTION6CC74 - 16774 - 167
10X-RAY DIFFRACTION7DD4 - 734 - 73
11X-RAY DIFFRACTION7DD168 - 348168 - 348
12X-RAY DIFFRACTION8DD74 - 16774 - 167
13X-RAY DIFFRACTION9EE4 - 734 - 73
14X-RAY DIFFRACTION9EE168 - 348168 - 348
15X-RAY DIFFRACTION10EE74 - 16774 - 167
16X-RAY DIFFRACTION11FF4 - 734 - 73
17X-RAY DIFFRACTION11FF168 - 348168 - 348
18X-RAY DIFFRACTION12FF74 - 16774 - 167
19X-RAY DIFFRACTION13GG4 - 734 - 73
20X-RAY DIFFRACTION13GG168 - 348168 - 348
21X-RAY DIFFRACTION14GG74 - 16774 - 167
22X-RAY DIFFRACTION15HH4 - 734 - 73
23X-RAY DIFFRACTION15HH168 - 348168 - 348
24X-RAY DIFFRACTION16HH74 - 16774 - 167
25X-RAY DIFFRACTION17II4 - 734 - 73
26X-RAY DIFFRACTION17II168 - 348168 - 348
27X-RAY DIFFRACTION18II74 - 16774 - 167
28X-RAY DIFFRACTION19JJ4 - 734 - 73
29X-RAY DIFFRACTION19JJ168 - 348168 - 348
30X-RAY DIFFRACTION20JJ74 - 16774 - 167
31X-RAY DIFFRACTION21KK4 - 734 - 73
32X-RAY DIFFRACTION21KK168 - 348168 - 348
33X-RAY DIFFRACTION22KK74 - 16774 - 167
34X-RAY DIFFRACTION23LL4 - 734 - 73
35X-RAY DIFFRACTION23LL168 - 348168 - 348
36X-RAY DIFFRACTION24LL74 - 16774 - 167
37X-RAY DIFFRACTION25MM4 - 734 - 73
38X-RAY DIFFRACTION25MM168 - 348168 - 348
39X-RAY DIFFRACTION26MM74 - 16774 - 167
40X-RAY DIFFRACTION27NN4 - 734 - 73
41X-RAY DIFFRACTION27NN168 - 348168 - 348
42X-RAY DIFFRACTION28NN74 - 16774 - 167
43X-RAY DIFFRACTION29OO5 - 735 - 73
44X-RAY DIFFRACTION29OO168 - 348168 - 348
45X-RAY DIFFRACTION30OO74 - 16774 - 167
46X-RAY DIFFRACTION31PP4 - 734 - 73
47X-RAY DIFFRACTION31PP168 - 348168 - 348
48X-RAY DIFFRACTION32PP74 - 16774 - 167

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • 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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