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- PDB-6nq4: Crystal structure of a Hydrolase, haloacid dehalogenase-like fami... -

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Basic information

Entry
Database: PDB / ID: 6nq4
TitleCrystal structure of a Hydrolase, haloacid dehalogenase-like family from Brucella suis 1330
ComponentsHAD superfamily hydrolase
KeywordsHYDROLASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyHAD-superfamily hydrolase, subfamily IIA, hypothetical 3 / HAD-superfamily hydrolase, subfamily IIA / Haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / hydrolase activity / PHOSPHATE ION / HAD superfamily hydrolase
Function and homology information
Biological speciesBrucella suis biovar 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of a Hydrolase, haloacid dehalogenase-like family from Brucella suis 1330
Authors: Abendroth, J. / Dranow, D.M. / Sankaran, B. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJan 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HAD superfamily hydrolase
B: HAD superfamily hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,97113
Polymers66,3392
Non-polymers63111
Water11,295627
1
A: HAD superfamily hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5367
Polymers33,1701
Non-polymers3666
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HAD superfamily hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4356
Polymers33,1701
Non-polymers2655
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.430, 60.120, 86.840
Angle α, β, γ (deg.)90.000, 104.280, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HAD superfamily hydrolase


Mass: 33169.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella suis biovar 1 (strain 1330) (bacteria)
Strain: 1330 / Gene: BS1330_II0196 / Plasmid: BrsuA.18142.a.A1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: A0A0H3GA96
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 627 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Rigaku Reagents Wizard 3/4 , condition B4: 200mM potassium citrate, tribasic, 20% PEG 3350: BrsuA.18142.a.A1.PS01295 at 20mg/ml: cryo: 20% EG: tray 229127 B4: puck: fbr1-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.99999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.45→35.057 Å / Num. obs: 107963 / % possible obs: 99.6 % / Redundancy: 4.018 % / Biso Wilson estimate: 25.469 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Rrim(I) all: 0.041 / Χ2: 1.05 / Net I/σ(I): 18.87
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.45-1.494.0740.483.0279650.8760.55399.9
1.49-1.534.0840.3454.0277800.930.39899.9
1.53-1.574.090.2615.2975020.9610.399.9
1.57-1.624.1070.216.6173900.9720.24299.8
1.62-1.674.1060.1628.4170790.9820.18699.8
1.67-1.734.1130.13410.1468730.9860.15499.8
1.73-1.84.110.10512.2866590.9920.12199.9
1.8-1.874.0950.0815.6863780.9950.09299.9
1.87-1.964.0760.06419.2461740.9960.07399.8
1.96-2.054.0270.05123.3458260.9970.05999.8
2.05-2.163.9890.04426.6355960.9980.0599.8
2.16-2.293.9560.03830.1852850.9980.04499.6
2.29-2.453.9130.03432.0449730.9980.0499.6
2.45-2.653.8970.03334.0946480.9980.03899.8
2.65-2.93.8620.03136.0542540.9980.03699.6
2.9-3.243.7860.02838.0438630.9980.03399.5
3.24-3.743.7710.02740.3134130.9990.03199.7
3.74-4.593.9460.02242.1829070.9990.02699.5
4.59-6.483.9030.02242.122600.9990.02599.6
6.48-35.0573.6250.02140.4211380.9990.02588

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(dev_3339)refinement
PDB_EXTRACT3.24data extraction
Arcimboldophasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Robetta model, followed up by Arcimboldo-shredder treatment

Resolution: 1.45→35.057 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.5
RfactorNum. reflection% reflectionSelection details
Rfree0.1835 2010 1.86 %0
Rwork0.1415 ---
obs0.1423 107954 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 65.14 Å2 / Biso mean: 25.1674 Å2 / Biso min: 11.75 Å2
Refinement stepCycle: final / Resolution: 1.45→35.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4003 0 37 647 4687
Biso mean--29.18 38.92 -
Num. residues----532
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.48630.20471450.157575357680100
1.4863-1.52650.20921320.148875487680100
1.5265-1.57140.17131320.139975107642100
1.5714-1.62210.21511570.130776317788100
1.6221-1.68010.17171310.123375077638100
1.6801-1.74730.18181530.132275537706100
1.7473-1.82690.1671490.12975427691100
1.8269-1.92320.1631460.124875637709100
1.9232-2.04370.16811350.124675497684100
2.0437-2.20140.16931540.134175877741100
2.2014-2.42290.17681380.135575847722100
2.4229-2.77340.21431450.153376097754100
2.7734-3.49370.17281560.149575987754100
3.4937-35.06740.19111370.14757628776598

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