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- PDB-3sl0: Crystal Structure of P. falciparum arginase complexed with 2-amin... -

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Basic information

Entry
Database: PDB / ID: 3sl0
TitleCrystal Structure of P. falciparum arginase complexed with 2-amino-6-borono-2-(difluoromethyl)hexanoic acid
ComponentsArginase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / metallohydrolase / arginase fold / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Urea cycle / Neutrophil degranulation / arginase / arginase activity / arginine catabolic process to ornithine / urea cycle / manganese ion binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Ureohydrolase domain / Ureohydrolase / Arginase family / Arginase family profile. / Arginase; Chain A / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-FB5 / : / Arginase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.997 Å
AuthorsDowling, D.P. / Ilies, M. / Christianson, D.W.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Binding of alpha , alpha-disubstituted amino acids to arginase suggests new avenues for inhibitor design.
Authors: Ilies, M. / Di Costanzo, L. / Dowling, D.P. / Thorn, K.J. / Christianson, D.W.
History
DepositionJun 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_atom_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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Sep 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7874
Polymers46,4521
Non-polymers3353
Water3,657203
1
A: Arginase
hetero molecules

A: Arginase
hetero molecules

A: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,36112
Polymers139,3563
Non-polymers1,0059
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area5860 Å2
ΔGint-30 kcal/mol
Surface area32280 Å2
MethodPISA
2
A: Arginase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)280,72124
Polymers278,7126
Non-polymers2,00918
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation10_545y+2/3,x-2/3,-z+1/31
crystal symmetry operation11_445x-y-1/3,-y-2/3,-z+1/31
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area14640 Å2
ΔGint-78 kcal/mol
Surface area61640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.959, 112.959, 229.760
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-482-

HOH

21A-528-

HOH

31A-578-

HOH

41A-601-

HOH

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Components

#1: Protein Arginase


Mass: 46452.039 Da / Num. of mol.: 1 / Fragment: UNP residues 22-411
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PFI0320w / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 Codonplustm(de3) Ril / References: UniProt: Q8I384, arginase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-FB5 / 2-(difluoromethyl)-6-(dihydroxyboranyl)-L-norleucine


Type: L-peptide linking / Mass: 224.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14BF2NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 3.04 Å3/Da / Density % sol: 59.49 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.2 M Na/K Phosphate (8.0), VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.997→50 Å / Num. all: 38494 / Num. obs: 38494 / % possible obs: 99.9 % / Redundancy: 7.8 % / Rsym value: 0.09 / Net I/σ(I): 23.6
Reflection shellResolution: 1.997→2.07 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 3757 / Rsym value: 0.587 / % possible all: 98.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MMR

3mmr


Resolution: 1.997→37.24 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1825 1920 4.99 %5%
Rwork0.1671 ---
obs0.1678 38478 99.75 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.569 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 35.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.6363 Å20 Å20 Å2
2--3.6363 Å20 Å2
3----7.2727 Å2
Refinement stepCycle: LAST / Resolution: 1.997→37.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2416 0 17 203 2636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062512
X-RAY DIFFRACTIONf_angle_d0.9223413
X-RAY DIFFRACTIONf_dihedral_angle_d12.53957
X-RAY DIFFRACTIONf_chiral_restr0.07391
X-RAY DIFFRACTIONf_plane_restr0.003437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9974-2.04730.29641430.25632516X-RAY DIFFRACTION97
2.0473-2.10270.24741600.22752548X-RAY DIFFRACTION100
2.1027-2.16450.22331280.19352588X-RAY DIFFRACTION100
2.1645-2.23440.18451470.16812566X-RAY DIFFRACTION100
2.2344-2.31420.19241260.15292613X-RAY DIFFRACTION100
2.3142-2.40690.17381220.16562614X-RAY DIFFRACTION100
2.4069-2.51640.2211480.15622600X-RAY DIFFRACTION100
2.5164-2.6490.1661440.15772586X-RAY DIFFRACTION100
2.649-2.8150.19831440.16922605X-RAY DIFFRACTION100
2.815-3.03220.18111230.17422622X-RAY DIFFRACTION100
3.0322-3.33720.18181400.17852621X-RAY DIFFRACTION100
3.3372-3.81970.17171400.1642623X-RAY DIFFRACTION100
3.8197-4.81070.15941320.13982674X-RAY DIFFRACTION100
4.8107-37.24660.16351230.16862782X-RAY DIFFRACTION100
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)
15.39170.1944-0.63244.49-0.48382.94460.0268-0.19860.14770.2819-0.0337-0.0675-0.6284-0.2634-0.03320.3431-0.0584-0.06410.0421-0.01710.13957.0813-2.996226.6539
26.95880.346-1.142.18540.07521.42670.102-0.16490.53470.2216-0.02080.3415-0.8118-0.3843-0.00950.43070.17150.01790.24980.01010.267941.49952.394621.786
31.088-0.09130.14612.5985-0.1251.89970.0202-0.04070.1422-0.0110.05560.4357-0.4187-0.5201-0.06410.2560.1110.00040.23290.03710.246238.9486-7.563815.9894
46.6101-1.97950.58375.5427-0.18054.1165-0.02730.1858-0.2449-0.46960.07180.19270.1431-0.2622-0.04570.1856-0.0313-0.04950.1194-0.00230.126946.028-22.10766.9074
50.92070.2222-0.04391.948-0.22112.6830.0401-0.0246-0.03940.0089-0.0283-0.0872-0.1759-0.0096-0.00230.1858-0.0005-0.01130.11640.02340.174153.3731-15.536417.398
64.576-1.1401-1.44592.06621.08975.7554-0.053-0.4099-0.36820.15930.0444-0.55840.01820.76860.0110.2172-0.0598-0.04890.19290.02790.294964.9082-16.427125.6793
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 22:71
2X-RAY DIFFRACTION2chain A and resid 154:185
3X-RAY DIFFRACTION3chain A and resid 186:280
4X-RAY DIFFRACTION4chain A and resid 281:309
5X-RAY DIFFRACTION5chain A and resid 310:374
6X-RAY DIFFRACTION6chain A and resid 375:411

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