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- PDB-4qku: Crystal structure of a putative hydrolase from Burkholderia cenoc... -

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Basic information

Entry
Database: PDB / ID: 4qku
TitleCrystal structure of a putative hydrolase from Burkholderia cenocepacia
Componentshydrolase
KeywordsHYDROLASE / National Institute of Allergy and Infectious Disease / NIAID / structural genomics / SSGCID / cystic fibrosis / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


ureidoglycolate lyase / ureidoglycolate lyase activity / fumarylacetoacetase / fumarylacetoacetase activity / tyrosine catabolic process / urate catabolic process / L-phenylalanine catabolic process
Similarity search - Function
Fumarylacetoacetase, N-terminal domain / Fumarylacetoacetase / Fumarylacetoacetase, N-terminal / Fumarylacetoacetase, N-terminal domain superfamily / Fumarylacetoacetase N-terminal / Fumarylacetoacetate hydrolase; domain 2 / Fumarylacetoacetase-like, C-terminal domain / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Fumarylacetoacetate (FAA) hydrolase family ...Fumarylacetoacetase, N-terminal domain / Fumarylacetoacetase / Fumarylacetoacetase, N-terminal / Fumarylacetoacetase, N-terminal domain superfamily / Fumarylacetoacetase N-terminal / Fumarylacetoacetate hydrolase; domain 2 / Fumarylacetoacetase-like, C-terminal domain / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Fumarylacetoacetate (FAA) hydrolase family / SH3 type barrels. / Roll / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of a putative hydrolase from Burkholderia cenocepacia
Authors: Edwards, T.E. / Fairman, J.W. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionJun 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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: hydrolase
B: hydrolase
C: hydrolase
D: hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,34017
Polymers191,5204
Non-polymers82113
Water10,917606
1
A: hydrolase
B: hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1228
Polymers95,7602
Non-polymers3626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-63 kcal/mol
Surface area29300 Å2
MethodPISA
2
C: hydrolase
D: hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2189
Polymers95,7602
Non-polymers4587
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-75 kcal/mol
Surface area29420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.640, 110.550, 116.160
Angle α, β, γ (deg.)90.000, 106.610, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERAA7 - 43215 - 440
21SERSERBB7 - 43215 - 440
12SERSERAA7 - 43215 - 440
22SERSERCC7 - 43215 - 440
13SERSERAA7 - 43215 - 440
23SERSERDD7 - 43215 - 440
14SERSERBB7 - 43215 - 440
24SERSERCC7 - 43215 - 440
15ARGARGBB7 - 43115 - 439
25ARGARGDD7 - 43115 - 439
16SERSERCC7 - 43215 - 440
26SERSERDD7 - 43215 - 440

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
hydrolase /


Mass: 47879.883 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: BAA-245 / Gene: BCAL3183 / Production host: Escherichia coli (E. coli) / References: UniProt: B4ECX4
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 606 / 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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4
Details: BuceA.00077.a.B1.PW37289 at 20.8 mg/mL against JCSG+ screen condition B1, 0.1 M Na citrate pH 4.0, 0.8 M ammonium sulfate cryo-protected with 20% ethylene glycol, crystal tracking ID ...Details: BuceA.00077.a.B1.PW37289 at 20.8 mg/mL against JCSG+ screen condition B1, 0.1 M Na citrate pH 4.0, 0.8 M ammonium sulfate cryo-protected with 20% ethylene glycol, crystal tracking ID 246960b1, unique puck ID rhw0-1, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 65624 / Num. obs: 65019 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 28.273 Å2 / Rmerge(I) obs: 0.146 / Χ2: 0.913 / Net I/σ(I): 10.06
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.45-2.510.5553.1423882476599
2.51-2.580.5063.4323053462598.5
2.58-2.660.4513.8422836455598.7
2.66-2.740.3774.4721729435598.6
2.74-2.830.3255.1421439431499.1
2.83-2.930.2666.0120410411999.3
2.93-3.040.2316.7619675399799.2
3.04-3.160.2017.7119062385399.2
3.16-3.30.1639.2718102370599.2
3.3-3.460.13111.217157352899.3
3.46-3.650.10913.0116364336999.2
3.65-3.870.09314.7915436319799.1
3.87-4.140.07717.0414421299499.5
4.14-4.470.06719.4313297278199.5
4.47-4.90.06619.2912534259799.4
4.9-5.480.07117.8511236231499.6
5.48-6.330.07317.1810127208199.2
6.33-7.750.06718.278484175499.4
7.75-10.960.04424.666470137199.5
10.960.04125.83319774596

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.35 Å47.89 Å
Translation5.35 Å47.89 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.6phasing
REFMAC5.8.0071refinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→50 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.888 / WRfactor Rfree: 0.2182 / WRfactor Rwork: 0.1817 / FOM work R set: 0.7935 / SU B: 19.202 / SU ML: 0.226 / SU R Cruickshank DPI: 0.6516 / SU Rfree: 0.2891 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.652 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2492 3174 4.9 %RANDOM
Rwork0.208 ---
obs0.21 65019 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.78 Å2 / Biso mean: 23.1 Å2 / Biso min: 2.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å2-0.4 Å2
2---0.62 Å2-0 Å2
3---1.55 Å2
Refinement stepCycle: LAST / Resolution: 2.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12686 0 45 606 13337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01913033
X-RAY DIFFRACTIONr_bond_other_d0.0050.0212135
X-RAY DIFFRACTIONr_angle_refined_deg1.3161.95217788
X-RAY DIFFRACTIONr_angle_other_deg0.964327764
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17751691
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.83923.135555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.445151874
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.43115105
X-RAY DIFFRACTIONr_chiral_restr0.070.21982
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02115118
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023063
X-RAY DIFFRACTIONr_mcbond_it0.9071.546776
X-RAY DIFFRACTIONr_mcbond_other0.9061.546775
X-RAY DIFFRACTIONr_mcangle_it1.592.3078460
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A241610.05
12B241610.05
21A242610.05
22C242610.05
31A242600.05
32D242600.05
41B243800.05
42C243800.05
51B248370.04
52D248370.04
61C246060.04
62D246060.04
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 233 -
Rwork0.281 4520 -
all-4753 -
obs--99.06 %
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)
10.7990.37220.08520.85610.21110.4714-0.07310.0246-0.1476-0.08040.067-0.19070.01470.08120.00610.0128-0.0010.02190.01570.00030.15439.7864-66.359125.1702
20.4897-0.1060.19220.43480.04440.66540.0026-0.01160.0028-0.0126-0.03630.0172-0.0438-0.10630.03370.00850.0172-0.01320.0432-0.00680.0746-21.6696-52.082422.9522
30.3568-0.1206-0.08470.48990.22760.42240.0397-0.0545-0.0155-0.0341-0.0068-0.10050.03880.0499-0.03280.01790.0057-0.00910.0188-0.00260.122318.9033-12.849832.7713
40.5545-0.09270.15490.3462-0.05290.4443-0.019-0.03410.0292-0.01450.0120.0354-0.0364-0.04660.0070.0070.0112-0.01050.0365-0.00060.0589-12.41891.918731.4784
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 432
2X-RAY DIFFRACTION2B6 - 432
3X-RAY DIFFRACTION3C7 - 432
4X-RAY DIFFRACTION4D7 - 433

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