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- PDB-6nfp: 1.7 Angstrom Resolution Crystal Structure of Arginase from Bacill... -

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Basic information

Entry
Database: PDB / ID: 6nfp
Title1.7 Angstrom Resolution Crystal Structure of Arginase from Bacillus subtilis subsp. subtilis str. 168
ComponentsArginase
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


arginine metabolic process / arginase / : / arginase activity / urea cycle / manganese ion binding / cytoplasm
Similarity search - Function
Arginase / Ureohydrolase domain / 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
FORMIC ACID / GLYCOLIC ACID / DI(HYDROXYETHYL)ETHER / UREA / Arginase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMinasov, G. / Wawrzak, Z. / Evdokimova, E. / Grimshaw, S. / Kwon, K. / Savchenko, A. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.7 Angstrom Resolution Crystal Structure of Arginase from Bacillus subtilis subsp. subtilis str. 168
Authors: Minasov, G. / Wawrzak, Z. / Evdokimova, E. / Grimshaw, S. / Kwon, K. / Savchenko, A. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 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.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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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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)200,277100
Polymers194,7966
Non-polymers5,48194
Water29,2381623
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, 2CEV
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30220 Å2
ΔGint-531 kcal/mol
Surface area55700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.414, 143.989, 85.515
Angle α, β, γ (deg.)90.00, 109.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Arginase


Mass: 32466.064 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rocF, BSU40320, argI / Plasmid: pMCSG53
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21 DE3 gold magic / References: UniProt: P39138, arginase

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Non-polymers , 10 types, 1717 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical
ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: CH4N2O
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#10: Chemical
ChemComp-GOA / GLYCOLIC ACID / HYDROXYACETIC ACID / HYDROXYETHANOIC ACID


Mass: 76.051 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O3
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1623 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein: 40.0 mg/ml, 0.3M Sodium chloride, 0.01M HEPES pH 7.5, Screen: 0.2M Magnesium chloride,0.1M Tris-HCL pH 8.5, 17% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 23, 2017 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 191464 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.032 / Rrim(I) all: 0.069 / Rsym value: 0.061 / Χ2: 1.026 / Net I/σ(I): 20.3
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.779 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 9654 / CC1/2: 0.618 / Rpim(I) all: 0.421 / Rrim(I) all: 0.887 / Rsym value: 0.779 / Χ2: 1.028 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-3000data reduction
HKL-3000data scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CEV

2cev


Resolution: 1.7→29.99 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.97 / SU B: 3.582 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.086 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16646 9706 5.1 %RANDOM
Rwork0.13946 ---
obs0.1408 181718 94.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.936 Å2
Baniso -1Baniso -2Baniso -3
1-2.79 Å20 Å20.21 Å2
2---1.37 Å20 Å2
3----1.25 Å2
Refinement stepCycle: 1 / Resolution: 1.7→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13179 0 314 1623 15116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01314033
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713258
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.63418893
X-RAY DIFFRACTIONr_angle_other_deg0.3661.58130906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.74351801
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.29124.397614
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.849152500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1911551
X-RAY DIFFRACTIONr_chiral_restr0.070.21804
X-RAY DIFFRACTIONr_gen_planes_refined0.0560.0215644
X-RAY DIFFRACTIONr_gen_planes_other0.0560.022473
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3772.0287151
X-RAY DIFFRACTIONr_mcbond_other1.3662.0197136
X-RAY DIFFRACTIONr_mcangle_it2.1183.0178959
X-RAY DIFFRACTIONr_mcangle_other2.1183.0178960
X-RAY DIFFRACTIONr_scbond_it2.5742.426882
X-RAY DIFFRACTIONr_scbond_other2.5742.4216883
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5113.4839935
X-RAY DIFFRACTIONr_long_range_B_refined6.26326.82715943
X-RAY DIFFRACTIONr_long_range_B_other6.06525.7215505
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 693 -
Rwork0.228 13193 -
obs--92.85 %
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)
10.80540.7914-0.21031.8902-0.12911.66750.007-0.05980.06840.07390.00760.0478-0.0019-0.0072-0.01460.00560.008-0.01240.1108-0.00020.1175-4.940116.761112.4503
23.81222.6632-0.46633.0887-0.87170.95620.2248-0.25050.12020.1738-0.14440.0925-0.1314-0.0416-0.08030.0309-0.00340.00160.0531-0.0290.0856-6.358523.349513.4447
30.77810.1198-0.04730.6307-0.00690.6509-0.01680.04120.0756-0.05360.00010.06280.0214-0.01630.01680.01440.0049-0.03020.08980.01980.0931-3.03414.1395-1.4176
41.2872-0.0951-0.49490.75770.04971.0648-0.0281-0.0055-0.03680.08920.0108-0.0460.05330.03860.01740.0178-0.0086-0.02840.11640.02370.123541.21210.540118.448
53.7157-1.9725-2.53852.13831.46872.788-0.0545-0.17450.07680.18140.0209-0.089-0.04270.12980.03360.0361-0.0239-0.02570.077-0.00790.09344.570224.258722.6922
60.58880.1490.04640.7471-0.07920.6762-0.00250.02680.0778-0.02320.01310.0122-0.0605-0.0156-0.01070.0093-0.0103-0.01230.10660.02880.115333.131321.05428.936
70.9283-0.4769-0.36970.9449-0.17151.0130.001-0.03310.1313-0.06320.0189-0.059-0.0153-0.0041-0.020.0181-0.0235-0.02330.10890.00340.11133.72446.884136.7008
82.6439-1.5873-1.40511.69860.86862.18990.14530.13780.2653-0.0537-0.102-0.1563-0.0642-0.0094-0.04330.0431-0.0251-0.01380.0968-0.01690.131535.354710.9540.2355
91.0396-0.0213-0.02450.5359-0.02930.5864-0.0172-0.122-0.00020.03930.0199-0.07670.08360.0066-0.00270.0303-0.0186-0.03020.11530.00550.060631.4577-3.768645.7561
101.04150.5178-0.33340.7455-0.2151.0187-0.05450.03150.0876-0.07230.03840.1609-0.0385-0.03050.01610.01160.0037-0.02390.1244-0.00190.1369-12.21658.255728.2506
114.96834.7122-1.05745.0947-1.12911.1357-0.0429-0.07360.1429-0.0586-0.00280.1493-0.158-0.11630.04560.03540.0233-0.00240.0514-0.01220.1585-16.641219.85235.0823
120.6809-0.1147-0.04790.7940.03040.85-0.0205-0.08560.09950.1104-0.00890.0974-0.02450.05070.02940.0167-0.0050.00790.1239-0.01280.0926-4.72218.297942.436
132.25440.0494-0.33760.585-0.28071.5052-0.0068-0.1191-0.13370.03490.00840.04490.1054-0.0744-0.00160.0169-0.00160.00220.01990.00990.075316.4122-20.742.9185
144.7941-1.63491.70671.4448-0.83182.7369-0.0385-0.1584-0.2940.00170.10640.18510.1305-0.2097-0.06790.0443-0.0248-0.01270.0310.00540.068913.3785-22.8754-1.497
150.8347-0.2652-0.25981.17510.24240.8350.05010.0049-0.0605-0.0835-0.0187-0.0780.00380.0609-0.03140.00870.0050.00320.0262-0.00110.03425.0813-13.72-5.6679
161.9059-0.1433-0.02610.7332-0.60482.23130.06510.1188-0.0344-0.0822-0.04910.00690.13440.0358-0.0160.01430.00920.00280.016-0.0070.037812.2962-26.872918.7551
173.56980.21652.15371.17690.01552.5806-0.0350.2872-0.0276-0.1162-0.0274-0.14220.08470.29320.06240.06920.04230.01910.0570.00570.0314.8574-30.72519.6565
180.80390.2065-0.17690.99210.05991.0140.05310.0194-0.06050.0509-0.04960.05610.1154-0.0452-0.00350.0263-0.0053-0.00120.01060.0080.04783.7265-27.642929.9304
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 34
2X-RAY DIFFRACTION2A35 - 56
3X-RAY DIFFRACTION3A61 - 296
4X-RAY DIFFRACTION4B-1 - 51
5X-RAY DIFFRACTION5B52 - 88
6X-RAY DIFFRACTION6B89 - 296
7X-RAY DIFFRACTION7C3 - 33
8X-RAY DIFFRACTION8C34 - 62
9X-RAY DIFFRACTION9C63 - 296
10X-RAY DIFFRACTION10D0 - 62
11X-RAY DIFFRACTION11D63 - 87
12X-RAY DIFFRACTION12D88 - 296
13X-RAY DIFFRACTION13E2 - 33
14X-RAY DIFFRACTION14E34 - 64
15X-RAY DIFFRACTION15E65 - 296
16X-RAY DIFFRACTION16F2 - 32
17X-RAY DIFFRACTION17F33 - 64
18X-RAY DIFFRACTION18F65 - 296

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