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- PDB-3sl1: Crystal Structure of P. falciparum arginase complexed with 2-amin... -

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Basic information

Entry
Database: PDB / ID: 3sl1
TitleCrystal Structure of P. falciparum arginase complexed with 2-amino-6-borono-2-methylhexanoic acid
ComponentsArginase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / metallohydrolase / arginase fold / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Urea cycle / Neutrophil degranulation / arginase / arginine catabolic process to ornithine / arginase activity / urea cycle / manganese ion binding / identical protein binding / nucleus / cytosol / cytoplasm
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
6-(dihydroxyboranyl)-2-methyl-L-norleucine / : / Arginase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.902 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 1.1Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Jul 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 1.3Sep 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)46,7514
Polymers46,4521
Non-polymers2993
Water3,819212
1
A: Arginase
hetero molecules

A: Arginase
hetero molecules

A: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,25312
Polymers139,3563
Non-polymers8979
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 area5880 Å2
ΔGint-31 kcal/mol
Surface area32010 Å2
MethodPISA
2
A: Arginase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)280,50624
Polymers278,7126
Non-polymers1,79318
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 area14700 Å2
ΔGint-81 kcal/mol
Surface area61090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.181, 113.181, 229.616
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-520-

HOH

21A-521-

HOH

31A-590-

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-FB6 / 6-(dihydroxyboranyl)-2-methyl-L-norleucine


Type: L-peptide linking / Mass: 189.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16BNO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.63 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.2 M Na/K Phosphate (pH 8.0), VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-E10.97918
SYNCHROTRONAPS 24-ID-E20.97918
SYNCHROTRONAPS 24-ID-E30.97918
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDApr 7, 2010
ADSC QUANTUM 3152CCDApr 7, 2010
ADSC QUANTUM 3153CCDApr 7, 2010
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 44684 / % possible obs: 99.9 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 23.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 3.4 / Num. unique all: 4393 / % possible all: 99.2

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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: 1.902→37.273 Å / SU ML: 0.45 / Isotropic thermal model: 31.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1817 2243 5.02 %5%
Rwork0.1629 ---
obs0.1638 44663 99.82 %-
Solvent computationShrinkage radii: 1.17 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.535 Å2 / ksol: 0.327 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.0635 Å20 Å2-0 Å2
2--3.0635 Å20 Å2
3----6.127 Å2
Refinement stepCycle: LAST / Resolution: 1.902→37.273 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2416 0 15 212 2643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072519
X-RAY DIFFRACTIONf_angle_d1.0523426
X-RAY DIFFRACTIONf_dihedral_angle_d12.815959
X-RAY DIFFRACTIONf_chiral_restr0.079394
X-RAY DIFFRACTIONf_plane_restr0.004439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.902-1.94310.25161410.23712585X-RAY DIFFRACTION98
1.9431-1.98830.23781230.20452627X-RAY DIFFRACTION100
1.9883-2.0380.23121210.18512627X-RAY DIFFRACTION100
2.038-2.09310.2211530.17492618X-RAY DIFFRACTION100
2.0931-2.15470.16751240.15892642X-RAY DIFFRACTION100
2.1547-2.22420.16121550.14922625X-RAY DIFFRACTION100
2.2242-2.30370.20841220.14312653X-RAY DIFFRACTION100
2.3037-2.39590.181290.15982663X-RAY DIFFRACTION100
2.3959-2.5050.19741540.15622601X-RAY DIFFRACTION100
2.505-2.6370.17121380.15352654X-RAY DIFFRACTION100
2.637-2.80220.18721430.16922654X-RAY DIFFRACTION100
2.8022-3.01840.19441440.17942651X-RAY DIFFRACTION100
3.0184-3.3220.2021630.18462648X-RAY DIFFRACTION100
3.322-3.80230.17951270.16122687X-RAY DIFFRACTION100
3.8023-4.78890.14611650.13562681X-RAY DIFFRACTION100
4.7889-37.27980.17081410.16152804X-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)
14.06270.2657-0.59253.1872-0.21472.62430.0789-0.08230.15960.2658-0.0564-0.1053-0.4601-0.142-0.03810.3572-0.0396-0.04060.0806-0.01380.143757.1912-3.080226.6321
24.2131-0.0031-0.70651.5875-0.04971.64160.1314-0.15610.46070.2248-0.01890.2694-0.6006-0.2809-0.07190.41220.12560.02810.2130.00960.26741.92962.394821.6701
31.0021-0.13980.08751.9741-0.14591.49350.0355-0.04490.0828-0.03680.02820.3291-0.3276-0.3945-0.05350.22650.09060.00240.19230.03980.217739.0988-7.800615.9775
43.9448-0.72240.54.4966-0.73112.8936-0.01740.1336-0.147-0.43890.09260.12760.0883-0.2255-0.06140.2064-0.0148-0.05630.14110.00010.145846.0966-22.05336.8644
50.84520.12720.20281.26410.19131.52910.0716-0.0128-0.03950.0019-0.0443-0.0874-0.19390.0134-0.02370.19520.0058-0.00370.11180.02810.166353.4611-15.694117.4804
62.5765-0.6308-0.95271.19250.99992.968-0.0353-0.3546-0.29880.1489-0.0091-0.40510.15070.53060.06140.251-0.0317-0.05010.18990.04730.271565.0187-16.51525.6663
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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