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- PDB-4f0l: Crystal structure of Amidohydrolase from Brucella melitensis -

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Basic information

Entry
Database: PDB / ID: 4f0l
TitleCrystal structure of Amidohydrolase from Brucella melitensis
ComponentsAmidohydrolase
KeywordsHYDROLASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / metal ion binding
Similarity search - Function
Formiminoglutamate deiminase / : / 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 / Roll ...Formiminoglutamate deiminase / : / 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 / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / FORMIC ACID / Amidohydrolase
Similarity search - Component
Biological speciesBrucella melitensis biovar Abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of Amidohydrolase from Brucella melitensis
Authors: Gardberg, A.S. / Abendroth, J. / Staker, B. / Stewart, L. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionMay 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Sep 13, 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_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_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: Amidohydrolase
B: Amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,1276
Polymers98,9232
Non-polymers2044
Water11,151619
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-4 kcal/mol
Surface area30580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.592, 62.192, 68.926
Angle α, β, γ (deg.)92.750, 95.490, 112.320
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Amidohydrolase


Mass: 49461.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis biovar Abortus (bacteria)
Strain: 2308 / Gene: BAB2_0307 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2YIL4
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 619 / 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: 2.15 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Internal tracking number 226312A8 (JCSG A8). Crystallant: 20% PEG3350, 200 mM ammonium formate. Protein: BrabA.17379.a.A1 PS01212 at 36.85 mg/ml in a buffer consisting of 25 mM Hepes pH 7.0, ...Details: Internal tracking number 226312A8 (JCSG A8). Crystallant: 20% PEG3350, 200 mM ammonium formate. Protein: BrabA.17379.a.A1 PS01212 at 36.85 mg/ml in a buffer consisting of 25 mM Hepes pH 7.0, 500 mM NaCl, 2 mM DTT, 0.025% sodium azide, and 5% glycerol., VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 18, 2011
RadiationMonochromator: Asymmetric curved crystal, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 49766 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.086 / Χ2: 1.088 / Net I/σ(I): 8.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.05-2.092.20.2113.824560.76596.5
2.09-2.122.20.18724590.77697.8
2.12-2.162.20.17524760.80196.8
2.16-2.212.20.16425200.86397.8
2.21-2.262.20.15224490.93697.5
2.26-2.312.20.1524760.95997
2.31-2.372.20.13124790.9998.2
2.37-2.432.20.12524841.04497.8
2.43-2.52.20.12624741.20597.4
2.5-2.582.20.11525031.16597.6
2.58-2.682.20.10325211.1898.3
2.68-2.782.20.09924691.29598.2
2.78-2.912.20.09124811.24597.7
2.91-3.062.20.08725061.18498
3.06-3.252.20.08124801.2897.8
3.25-3.512.20.07624791.16798.1
3.51-3.862.10.06925111.24598
3.86-4.422.10.06725041.27598.6
4.42-5.562.20.06425251.21599.1
5.56-502.20.06425141.19699.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å49.2 Å
Translation2.5 Å49.2 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MDU

3mdu


Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.586 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.184 2531 5.1 %RANDOM
Rwork0.148 ---
obs0.15 49766 97.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.396 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0.18 Å20.08 Å2
2---0.48 Å2-0.28 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6762 0 8 619 7389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196945
X-RAY DIFFRACTIONr_bond_other_d0.0040.024607
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.9389425
X-RAY DIFFRACTIONr_angle_other_deg1.119311131
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1075905
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.31823.252329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.328151058
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3831559
X-RAY DIFFRACTIONr_chiral_restr0.0860.21023
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028055
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021516
LS refinement shellResolution: 2.053→2.107 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.193 187 -
Rwork0.154 3348 -
all-3535 -
obs-2489 93.92 %
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)
10.5003-0.49640.40231.117-0.20320.95130.0006-0.0132-0.0176-0.08620.0584-0.00540.0143-0.0688-0.0590.0192-0.0130.01570.06370.01310.057616.95371.767-14.0614
20.6283-0.495-0.25651.39850.07210.32150.01750.0432-0.0343-0.0539-0.0198-0.05950.03970.00470.00240.04090.00760.0060.0503-0.02010.036627.2262-19.1672-18.7101
31.6086-0.29490.07160.69320.07560.320.00730.01720.0752-0.03040.0298-0.17660.01680.0539-0.0370.00730.00190.02160.0466-0.0060.110339.2132-3.6991-14.071
40.6014-0.07730.0640.89710.51741.3791-0.01750.03370.0337-0.05180.0509-0.0751-0.10890.0812-0.03340.03450.00250.00550.03270.02440.047723.61019.6038-11.7313
50.8482-0.333-0.03982.2459-0.69921.2513-0.0188-0.02340.00990.15380.07960.21220.0412-0.1366-0.06070.0192-0.0080.01470.056-0.00970.04159.0999-9.2358-9.0401
60.57280.3522-0.46530.6607-0.20191.2865-0.0112-0.04210.00080.0913-0.0261-0.01750.0484-0.06090.03730.037-0.0022-0.01510.02790.00060.01416.23420.268316.1924
70.86060.40910.24081.46490.23910.75130.0406-0.06590.10930.0466-0.0527-0.0348-0.2043-0.01040.01210.1311-0.01560.00970.0197-0.01280.022324.448322.610720.5219
81.50480.25320.02981.26230.14490.60930.0273-0.0645-0.00710.0970.0206-0.2365-0.04050.1139-0.04790.0275-0.0108-0.03970.0669-0.00970.085238.03468.371216.7463
90.73660.1318-0.68990.7270.73932.21350.0054-0.017-0.08530.17870.0147-0.11630.20840.0244-0.02010.0620.0103-0.02840.03520.02130.043823.7936-6.323614.0125
100.76120.4980.27593.7162-0.30652.08770.0157-0.0119-0.0019-0.2780.07850.3359-0.1224-0.4253-0.09420.07710.043-0.01090.11740.00220.067.791410.835310.7492
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 86
2X-RAY DIFFRACTION2A87 - 237
3X-RAY DIFFRACTION3A238 - 339
4X-RAY DIFFRACTION4A340 - 417
5X-RAY DIFFRACTION5A418 - 454
6X-RAY DIFFRACTION6B6 - 86
7X-RAY DIFFRACTION7B87 - 237
8X-RAY DIFFRACTION8B238 - 339
9X-RAY DIFFRACTION9B340 - 417
10X-RAY DIFFRACTION10B418 - 454

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