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- PDB-4g7e: Crystal structure of pigeon pea urease -

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Basic information

Entry
Database: PDB / ID: 4g7e
TitleCrystal structure of pigeon pea urease
Components(urease) x 2
KeywordsHYDROLASE / Urease / pigeon pea / TIM barrel domain / B domain / Catalyzes urea hydrolysis to ammonia / carbon di-oxide
Function / homology
Function and homology information


urease / urease activity / urea catabolic process / nickel cation binding
Similarity search - Function
Urease / Urease subunit beta-alpha, linker domain / Urease subunit beta-alpha linker domain / Urease, subunit B / Urease, beta subunit / Urease; subunit A / Urease, gamma-like subunit / Urease active site / Urease active site. / Urease nickel binding site ...Urease / Urease subunit beta-alpha, linker domain / Urease subunit beta-alpha linker domain / Urease, subunit B / Urease, beta subunit / Urease; subunit A / Urease, gamma-like subunit / Urease active site / Urease active site. / Urease nickel binding site / Urease nickel ligands signature. / Urease, beta subunit / Urease, alpha subunit / Urease alpha subunit, C-terminal / Urease, beta subunit superfamily / Urease beta subunit / Urease domain profile. / Urease alpha-subunit, N-terminal domain / Urease alpha-subunit, N-terminal domain / Urease, gamma/gamma-beta subunit / Urease, gamma subunit superfamily / Urease, gamma subunit / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Ribbon / Roll / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Urease
Similarity search - Component
Biological speciesCajanus cajan (pigeon pea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBalasubramanian, A. / Ponnuraj, K.
CitationJournal: Int.J.Biol.Macromol. / Year: 2013
Title: Structural and functional studies on urease from pigeon pea (Cajanus cajan)
Authors: Balasubramanian, A. / Durairajpandian, V. / Elumalai, S. / Mathivanan, N. / Munirajan, A.K. / Ponnuraj, K.
History
DepositionJul 20, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: urease
B: urease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,4107
Polymers180,1512
Non-polymers2595
Water11,818656
1
A: urease
B: urease
hetero molecules

A: urease
B: urease
hetero molecules

A: urease
B: urease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)541,23121
Polymers540,4536
Non-polymers77715
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area67610 Å2
ΔGint-434 kcal/mol
Surface area126450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.292, 176.292, 346.438
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 840
2111B1 - 840

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Components

#1: Protein urease


Mass: 90051.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cajanus cajan (pigeon pea) / References: UniProt: I3PA93*PLUS, urease
#2: Protein urease


Mass: 90099.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cajanus cajan (pigeon pea) / References: UniProt: I3PA93*PLUS, urease
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 656 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE DATABASE REFERENCES FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. CHAIN B HAS CME AT 207TH RESIDUE.

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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: 2.88 Å3/Da / Density % sol: 57.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 23% PEG2KMME, 1M MgCl2, 100mM Tris, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 21, 2008 / Details: mirrors
RadiationMonochromator: yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 133788 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.17 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 5.4
Reflection shellHighest resolution: 2.2 Å / Rmerge(I) obs: 0.097 / Mean I/σ(I) obs: 5.4 / Num. unique all: 133788 / Rsym value: 0.0417 / % possible all: 96.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5refinement
AUTOMARdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→29.7 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.91 / SU B: 7.346 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26784 5178 5 %RANDOM
Rwork0.21716 ---
obs0.21969 98271 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.479 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12510 0 5 656 13171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02212730
X-RAY DIFFRACTIONr_angle_refined_deg1.8141.96817266
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.72651660
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.72324.672518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.749152121
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6291568
X-RAY DIFFRACTIONr_chiral_restr0.1130.22002
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219550
X-RAY DIFFRACTIONr_mcbond_it0.6491.58240
X-RAY DIFFRACTIONr_mcangle_it1.237213266
X-RAY DIFFRACTIONr_scbond_it2.26234490
X-RAY DIFFRACTIONr_scangle_it3.6234.54000
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 6246 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.10.05
tight thermal0.230.5
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 337 -
Rwork0.32 7031 -
obs--96.6 %

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