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- PDB-3mmr: Structure of Plasmodium falciparum Arginase in complex with ABH -

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Basic information

Entry
Database: PDB / ID: 3mmr
TitleStructure of Plasmodium falciparum Arginase in complex with ABH
ComponentsArginase
KeywordsHYDROLASE / malaria / ABH / LCR / parasite / L-arginine / boronic acid / metallohydrolase / binuclear / manganese
Function / homology
Function and homology information


Urea cycle / Neutrophil degranulation / arginase / : / arginase activity / urea cycle / manganese ion binding / identical protein binding / 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
2(S)-AMINO-6-BORONOHEXANOIC ACID / BETA-MERCAPTOETHANOL / : / Arginase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsDowling, D.P. / Ilies, M. / Olszewski, K.L. / Portugal, S. / Mota, M.M. / Llinas, M. / Christianson, D.W.
CitationJournal: Biochemistry / Year: 2010
Title: Crystal structure of arginase from Plasmodium falciparum and implications for L-arginine depletion in malarial infection .
Authors: Dowling, D.P. / Ilies, M. / Olszewski, K.L. / Portugal, S. / Mota, M.M. / Llinas, M. / Christianson, D.W.
History
DepositionApr 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / 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 / _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

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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)46,8325
Polymers46,4521
Non-polymers3804
Water5,368298
1
A: Arginase
hetero molecules

A: Arginase
hetero molecules

A: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,49615
Polymers139,3563
Non-polymers1,14012
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 area9160 Å2
ΔGint-70 kcal/mol
Surface area31370 Å2
MethodPISA
2
A: Arginase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)280,99230
Polymers278,7126
Non-polymers2,28024
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 area21110 Å2
ΔGint-157 kcal/mol
Surface area59940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.594, 112.594, 228.900
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-615-

HOH

21A-616-

HOH

31A-706-

HOH

41A-707-

HOH

51A-710-

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 3D7 (eukaryote) / Strain: isolate 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-ABH / 2(S)-AMINO-6-BORONOHEXANOIC ACID


Mass: 191.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15BNO5
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.08 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.4 M Na/K Phosphate (pH 8.0), VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.14→49.354 Å / Num. all: 59546 / Num. obs: 31095 / % possible obs: 100 % / Redundancy: 8.4 % / Biso Wilson estimate: 28.8 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 19.4
Reflection shellResolution: 2.14→2.23 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 5.4 / Num. unique all: 3052 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1PQ3

1pq3


Resolution: 2.14→37.112 Å / SU ML: 0.2 / Isotropic thermal model: isotropic / σ(F): 0.14 / Phase error: 17.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1862 2978 9.9 %random
Rwork0.1555 ---
obs0.1586 30079 96.56 %-
all-59546 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.712 Å2 / ksol: 0.329 e/Å3
Displacement parametersBiso mean: 32.8 Å2
Baniso -1Baniso -2Baniso -3
1-4.1157 Å2-0 Å2-0 Å2
2--4.1157 Å20 Å2
3----8.2315 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2.14→37.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2416 0 19 298 2733
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072504
X-RAY DIFFRACTIONf_angle_d1.113400
X-RAY DIFFRACTIONf_dihedral_angle_d17.073930
X-RAY DIFFRACTIONf_chiral_restr0.078389
X-RAY DIFFRACTIONf_plane_restr0.004435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.17470.20121050.16851186X-RAY DIFFRACTION88
2.1747-2.21210.21821390.16411194X-RAY DIFFRACTION91
2.2121-2.25240.21441600.16121191X-RAY DIFFRACTION92
2.2524-2.29570.19081410.15671256X-RAY DIFFRACTION94
2.2957-2.34250.22451260.16841246X-RAY DIFFRACTION95
2.3425-2.39350.1991200.1611290X-RAY DIFFRACTION95
2.3935-2.44910.22241340.16911261X-RAY DIFFRACTION95
2.4491-2.51040.18881550.15761254X-RAY DIFFRACTION95
2.5104-2.57820.1981380.15831273X-RAY DIFFRACTION97
2.5782-2.65410.19481430.15811286X-RAY DIFFRACTION97
2.6541-2.73970.19881460.16261303X-RAY DIFFRACTION97
2.7397-2.83760.18751530.16741271X-RAY DIFFRACTION98
2.8376-2.95120.20521230.16591340X-RAY DIFFRACTION98
2.9512-3.08540.22281390.18711296X-RAY DIFFRACTION98
3.0854-3.2480.24511480.17741324X-RAY DIFFRACTION99
3.248-3.45140.17871720.15911304X-RAY DIFFRACTION99
3.4514-3.71760.19881460.14141335X-RAY DIFFRACTION100
3.7176-4.09130.1431450.1361337X-RAY DIFFRACTION99
4.0913-4.68230.13861430.12051348X-RAY DIFFRACTION100
4.6823-5.89540.1581530.14311382X-RAY DIFFRACTION100
5.8954-37.11730.17871490.16081424X-RAY DIFFRACTION99

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