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- PDB-6nbk: Crystal structure of Arginase from Bacillus cereus -

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Basic information

Entry
Database: PDB / ID: 6nbk
TitleCrystal structure of Arginase from Bacillus cereus
ComponentsArginase
KeywordsHYDROLASE / CSGID / structural genomics / arginase / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


arginine metabolic process / arginase / arginase activity / urea cycle / metal ion binding
Similarity search - Function
Ureohydrolase domain / Arginase / Ureohydrolase, manganese-binding site / Arginase family signature. / Ureohydrolase / Arginase family / Arginase family profile. / Arginase; Chain A / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus thuringiensis DB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsChang, C. / Evdokimova, E. / Mcchesney, M. / Joachimiak, A. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of Arginase from Bacillus cereus
Authors: Chang, C. / Evdokimova, E. / Mcchesney, M. / Joachimiak, A.
History
DepositionDec 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pH / _exptl_crystal_grow.pdbx_details
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_asym_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arginase
B: Arginase
C: Arginase
D: Arginase
E: Arginase
F: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,98823
Polymers194,0996
Non-polymers88917
Water29,0941615
1
A: Arginase
B: Arginase
C: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,60914
Polymers97,0493
Non-polymers56011
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-59 kcal/mol
Surface area30290 Å2
2
D: Arginase
E: Arginase
F: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3799
Polymers97,0493
Non-polymers3306
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-47 kcal/mol
Surface area30220 Å2
3


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13970 Å2
ΔGint-137 kcal/mol
Surface area56230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.022, 153.803, 83.137
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Arginase /


Mass: 32349.789 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis DB27 (bacteria) / Gene: BTDB27_005763 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: W8YSI5, arginase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1615 / 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: 2.44 Å3/Da / Density % sol: 49.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG3350 25%, 0.2M NH4Acte, 0.1M BisTr

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 29, 2017
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 144946 / % possible obs: 99 % / Redundancy: 5.9 % / Biso Wilson estimate: 18.45 Å2 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.027 / Rrim(I) all: 0.067 / Χ2: 0.866 / Net I/σ(I): 13.1 / Num. measured all: 848033
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.934.40.59565750.7990.2950.6680.991.2
1.93-1.974.60.55570110.8490.2720.6210.88896.1
1.97-2.014.90.46871270.9080.2260.5220.89999.2
2.01-2.055.10.41972290.9370.1980.4650.9299.6
2.05-2.095.40.38271710.9520.1770.4220.92699.3
2.09-2.145.50.32372200.9560.1490.3570.93199
2.14-2.195.70.27771430.9720.1250.3050.9398.6
2.19-2.256.30.24672520.980.1070.2680.93399.9
2.25-2.326.30.19572680.9850.0850.2130.936100
2.32-2.396.30.16372650.9870.070.1780.924100
2.39-2.486.20.13572570.9890.0590.1480.923100
2.48-2.586.10.10373190.9930.0450.1120.89299.6
2.58-2.760.08871920.9920.0390.0970.85999.1
2.7-2.846.40.07273300.9940.0310.0780.836100
2.84-3.026.40.06273160.9950.0260.0670.824100
3.02-3.256.30.05473510.9950.0230.0590.816100
3.25-3.5860.04973170.9940.0210.0530.85599.6
3.58-4.096.60.04574070.9960.0190.0480.77999.9
4.09-5.166.10.04374590.9950.0190.0470.71699.7
5.16-506.20.04977370.9930.0220.0540.72999.7

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1cev.pdb
Resolution: 1.91→48.444 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.62
RfactorNum. reflection% reflection
Rfree0.2034 6774 4.96 %
Rwork0.1611 --
obs0.1631 136503 92.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.59 Å2 / Biso mean: 23.163 Å2 / Biso min: 3.63 Å2
Refinement stepCycle: final / Resolution: 1.91→48.444 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13058 0 17 1615 14690
Biso mean--20.85 33.67 -
Num. residues----1726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613300
X-RAY DIFFRACTIONf_angle_d0.77717981
X-RAY DIFFRACTIONf_chiral_restr0.0542073
X-RAY DIFFRACTIONf_plane_restr0.0052335
X-RAY DIFFRACTIONf_dihedral_angle_d13.7317980
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9103-1.9320.2628960.20431923201941
1.932-1.95470.25611490.20562893304263
1.9547-1.97860.24651990.19833115331468
1.9786-2.00360.21031670.19563413358074
2.0036-2.030.25181950.18973645384079
2.03-2.05780.24072210.18313858407984
2.0578-2.08720.23672090.18784057426688
2.0872-2.11840.23232250.18394332455793
2.1184-2.15150.22392230.17434472469596
2.1515-2.18670.23422370.17224481471897
2.1867-2.22440.21222220.173646114833100
2.2244-2.26490.24712220.169246534875100
2.2649-2.30840.2232330.16646254858100
2.3084-2.35560.22822140.164846384852100
2.3556-2.40680.212670.161446164883100
2.4068-2.46280.21752390.163446614900100
2.4628-2.52440.19772550.161146244879100
2.5244-2.59260.20362390.16284603484299
2.5926-2.66890.23542480.17344601484999
2.6689-2.7550.22952630.165746264889100
2.755-2.85350.21812460.161146614907100
2.8535-2.96770.19792330.161447024935100
2.9677-3.10280.21472470.171446404887100
3.1028-3.26630.20592340.159246934927100
3.2663-3.47090.1742270.15364698492599
3.4709-3.73880.18582460.147946824928100
3.7388-4.11490.18122530.136447194972100
4.1149-4.70990.15912370.126447564993100
4.7099-5.93220.1662650.147647735038100
5.9322-48.45980.19992630.17474958522199
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)
10.001-0.000600.0014-0.00080.00090.00470.00080.02230.00080.0139-0.01280.0004-0.0031-00.09260.0310.00970.10790.02550.0851175.516969.1242-34.5131
20.0029-0.0012-0.00210.00250.00070.002-0.00740.0085-0.003-0.0101-0.0095-0.00940.0119-0.0028-0.01110.06440.03660.00750.10210.00490.0227173.14358.397-42.3287
30.0023-0.0025-0.00080.00510.00040.00350.00950.01250.0204-0.00460.005-0.0103-0.0073-0.00620.02390.08810.02930.0020.09460.08140.1068173.630378.3848-37.2258
40.0041-0.0016-0.00350.005100.00410.00320.00310.0071-0.01470.00420.00430.00580.0040.00330.05930.05530.01250.10040.08140.0467165.703971.7782-38.374
50.0045-0.0031-0.00060.0020.00110.00130.0078-0.00060.01620.01070.00370.0035-0.0067-0.0106-0.00030.09330.05870.01660.10150.0250.0731162.432572.8897-25.9733
60.003-0.0059-0.00330.01020.00740.0050.00870.00720.03650.01380.0181-0.0051-0.0069-0.01430.01950.0720.08680.00830.06440.02980.0618164.210977.7284-25.4221
70.007-0.0026-0.00130.0073-0.00950.0146-0.0193-0.0062-0.0020.03170.00550.0142-0.0085-0.0313-0.01490.07360.06220.05150.1050.01410.0709156.982165.4561-21.5499
80.00140.00080.00020.00130.00150.00320.0023-0.0033-0.00160.0041-0.0001-0.0013-0.00010.0030.00040.10110.03030.00070.0630.01010.0221172.844557.4005-20.497
90.0007-0.000700.00050.00010.0002-0.00360.0017-0.00340.0028-0.00130.00620.0031-0.0001-0.00010.05330.00160.01360.0835-0.00780.0443159.398153.0849-30.0795
100.00190.00070.00130.0019-0.00030.00450.00120.0085-0.00420.0024-0.0072-0.0030.0096-0.0056-0.00280.07440.03210.00530.08690.01920.026169.463656.8015-33.2515
110.00420.00110.01220.01040.00110.0453-0.03790.0461-0.08420.0089-0.02880.0460.0172-0.004-0.05280.0755-0.06990.04010.0157-0.1450.2236173.437118.8944-27.2142
120.0004-0.00030.00050.0005-0.00030.0012-0.00180.0099-0.0014-0.0012-0.00010.0075-0.00290.0031-0.00080.0915-0.0452-0.01830.1084-0.0820.1532161.595626.9267-34.2354
130.06590.01050.00250.00750.0019-0.0014-0.02190.0712-0.0958-0.0109-0.03270.14-0.0099-0.0672-0.0152-0.0312-0.118-0.0599-0.062-0.16210.1371163.466631.0448-27.5343
140.01320.0071-0.01090.0077-0.00940.0175-0.0077-0.07690.01640.0172-0.0333-0.00440.00010.0111-0.02990.1152-0.00520.00480.192-0.04830.0269179.984554.46129.9851
150.00830.0016-0.00060.0006-0.0020.0059-0.0004-0.0516-0.01320.0146-0.0025-0.0021-0.0089-0.00740.00390.1425-0.04240.05920.2390.00580.0082171.233946.409711.4246
160.01440.0116-0.01260.0049-0.00750.00820.0055-0.1051-0.04330.0428-0.01980.03030.0215-0.0386-0.00190.0586-0.07910.11590.18170.0302-0.0707164.871242.9234.5745
170.0012-0.00020.00220.0007-0.00010.0049-0.0049-0.0040.0055-0.00290.00040.0035-0.0035-0.0088-0.00030.1150.00150.04040.1362-0.01260.0442162.497956.3273-5.1007
180.00390.0039-0.0010.0046-0.00340.0155-0.0113-0.00950.00170.0004-0.02090.0039-0.0006-0.0045-0.02930.0841-0.01910.02770.1194-0.03050.0059173.87556.0038-1.9616
190.0256-0.01750.00460.0125-0.01140.0319-0.01830.0640.0787-0.011-0.0421-0.0533-0.00340.0095-0.05690.09010.03450.02910.06360.09250.1272194.722168.9674-41.1867
200.0125-0.01060.00880.0092-0.00880.008-0.01090.03350.0222-0.0183-0.0313-0.03320.02060.0099-0.04210.11930.05860.10250.09480.13880.1481203.014162.5253-46.8905
210.02510.0015-0.02250.007-0.00530.01930.01230.0890.0913-0.0563-0.0649-0.19030.03830.0621-0.03480.07010.0310.0407-0.01190.17540.1204207.480657.97-38.8222
220.00360.0016-0.00010.00170.00260.0043-0.0128-0.02810.0220.0119-0.01340.01670.0193-0.00700.13310.0152-0.00490.0967-0.01140.086200.258848.84084.3057
230.01350.0072-0.00730.01060.00520.0128-0.0326-0.04960.07190.02420.0314-0.0001-0.02230.01740.01070.13790.0022-0.05250.0927-0.08840.1225207.053863.28245.905
240.0134-0.0022-0.00330.01190.00130.0224-0.03690.01030.08740.0060.03-0.04650.0010.0916-0.00090.0869-0.014-0.01390.069-0.01250.0749211.860255.0373-6.6494
250.001-0.00150.00090.00550.00260.01080.01310.019-0.04330.0140.00620.00910.0236-0.01370.03070.0871-0.02240.010.067-0.10290.1034196.445719.1902-29.6196
260.03790.0037-0.00130.00660.00450.0096-0.01390.028-0.08610.0627-0.0066-0.04020.0362-0.0004-0.02350.0935-0.0032-0.0062-0.023-0.06980.0711208.690925.8678-23.4208
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 20 )A3 - 20
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 46 )A21 - 46
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 86 )A47 - 86
4X-RAY DIFFRACTION4chain 'A' and (resid 87 through 111 )A87 - 111
5X-RAY DIFFRACTION5chain 'A' and (resid 112 through 130 )A112 - 130
6X-RAY DIFFRACTION6chain 'A' and (resid 131 through 177 )A131 - 177
7X-RAY DIFFRACTION7chain 'A' and (resid 178 through 227 )A178 - 227
8X-RAY DIFFRACTION8chain 'A' and (resid 228 through 245 )A228 - 245
9X-RAY DIFFRACTION9chain 'A' and (resid 246 through 259 )A246 - 259
10X-RAY DIFFRACTION10chain 'A' and (resid 260 through 297 )A260 - 297
11X-RAY DIFFRACTION11chain 'B' and (resid 3 through 111 )B3 - 111
12X-RAY DIFFRACTION12chain 'B' and (resid 112 through 130 )B112 - 130
13X-RAY DIFFRACTION13chain 'B' and (resid 131 through 297 )B131 - 297
14X-RAY DIFFRACTION14chain 'C' and (resid 3 through 86 )C3 - 86
15X-RAY DIFFRACTION15chain 'C' and (resid 87 through 140 )C87 - 140
16X-RAY DIFFRACTION16chain 'C' and (resid 141 through 245 )C141 - 245
17X-RAY DIFFRACTION17chain 'C' and (resid 246 through 259 )C246 - 259
18X-RAY DIFFRACTION18chain 'C' and (resid 260 through 296 )C260 - 296
19X-RAY DIFFRACTION19chain 'D' and (resid 3 through 86 )D3 - 86
20X-RAY DIFFRACTION20chain 'D' and (resid 87 through 140 )D87 - 140
21X-RAY DIFFRACTION21chain 'D' and (resid 141 through 296 )D141 - 296
22X-RAY DIFFRACTION22chain 'E' and (resid 3 through 46 )E3 - 46
23X-RAY DIFFRACTION23chain 'E' and (resid 47 through 154 )E47 - 154
24X-RAY DIFFRACTION24chain 'E' and (resid 155 through 297 )E155 - 297
25X-RAY DIFFRACTION25chain 'F' and (resid 2 through 86 )F2 - 86
26X-RAY DIFFRACTION26chain 'F' and (resid 87 through 297 )F87 - 297

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