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- PDB-4uat: Crystal structure of CbbY (mutant D10N) from Rhodobacter sphaeroi... -

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Basic information

Entry
Database: PDB / ID: 4uat
TitleCrystal structure of CbbY (mutant D10N) from Rhodobacter sphaeroides in complex with Xylulose-(1,5)bisphosphate, crystal form I
ComponentsProtein CbbY
KeywordsHYDROLASE / haloacid dehalogenase (HAD) hydrolase superfamily / phosphatase
Function / homology
Function and homology information


xylulose catabolic process / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / hydrolase activity / magnesium ion binding
Similarity search - Function
Protein CbbY-like / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 ...Protein CbbY-like / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
XYLULOSE-1,5-BISPHOSPHATE / Protein CbbY
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsBracher, A. / Sharma, A. / Starling-Windhof, A. / Hartl, F.U. / Hayer-Hartl, M.
CitationJournal: Nat.Plants / Year: 2015
Title: Degradation of potent Rubisco inhibitor by selective sugar phosphatase.
Authors: Bracher, A. / Sharma, A. / Starling-Windhof, A. / Hartl, F.U. / Hayer-Hartl, M.
History
DepositionAug 11, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Dec 20, 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein CbbY
B: Protein CbbY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3618
Polymers50,3022
Non-polymers1,0596
Water11,728651
1
A: Protein CbbY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6804
Polymers25,1511
Non-polymers5303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein CbbY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6804
Polymers25,1511
Non-polymers5303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.419, 51.468, 122.083
Angle α, β, γ (deg.)90.000, 94.060, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is a monomer

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Components

#1: Protein Protein CbbY


Mass: 25150.752 Da / Num. of mol.: 2 / Mutation: D10N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: cbbY / Plasmid: pHue / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P95649
#2: Sugar ChemComp-XBP / XYLULOSE-1,5-BISPHOSPHATE


Type: saccharide / Mass: 310.090 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O11P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 651 / 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: 2.21 Å3/Da / Density % sol: 44.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25 % PEG-550MME, 0.1 M MES-NaOH pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97639 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97639 Å / Relative weight: 1
ReflectionResolution: 1.3→121.776 Å / Num. all: 107256 / Num. obs: 107256 / % possible obs: 99.5 % / Redundancy: 4.7 % / Rpim(I) all: 0.033 / Rrim(I) all: 0.074 / Rsym value: 0.066 / Net I/av σ(I): 8.931 / Net I/σ(I): 13.2 / Num. measured all: 506407
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.3-1.374.20.8390.963459152680.4510.8391.997.4
1.37-1.454.50.5751.367243147900.2990.5752.899.7
1.45-1.5550.356269217139430.1770.3564.699.9
1.55-1.6850.2283.164324129810.1130.2286.8100
1.68-1.844.60.1444.955200119460.0750.1449.799.7
1.84-2.064.80.0838.552065108120.0420.08315.7100
2.06-2.3750.05512.64827095900.0280.05523.6100
2.37-2.914.90.04316.13964681100.0220.04329.499.9
2.91-4.114.50.0320.22834962650.0160.0341.599.5
4.11-40.5925.20.02622.71863435510.0120.02650.799.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å40.59 Å
Translation3 Å40.59 Å

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
MOLREP10.2.35phasing
PDB_EXTRACT3.14data extraction
REFMAC5.7.0029refinement
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4UAR

4uar


Resolution: 1.3→30 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.969 / WRfactor Rfree: 0.1571 / WRfactor Rwork: 0.1135 / FOM work R set: 0.9162 / SU B: 1.569 / SU ML: 0.029 / SU R Cruickshank DPI: 0.0424 / SU Rfree: 0.0462 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1685 5342 5 %RANDOM
Rwork0.1212 101844 --
obs0.1235 107186 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 88.93 Å2 / Biso mean: 16.916 Å2 / Biso min: 5.64 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å2-0 Å2-0.2 Å2
2---0.26 Å20 Å2
3----0.79 Å2
Refinement stepCycle: final / Resolution: 1.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3466 0 62 661 4189
Biso mean--17.16 32.71 -
Num. residues----450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0193779
X-RAY DIFFRACTIONr_bond_other_d0.0010.023652
X-RAY DIFFRACTIONr_angle_refined_deg2.0491.9935141
X-RAY DIFFRACTIONr_angle_other_deg0.95538389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2445483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.41322.247178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01815627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7551548
X-RAY DIFFRACTIONr_chiral_restr0.2490.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0214326
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02870
X-RAY DIFFRACTIONr_rigid_bond_restr6.03437431
X-RAY DIFFRACTIONr_sphericity_free35.8065143
X-RAY DIFFRACTIONr_sphericity_bonded11.34857870
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 388 -
Rwork0.293 7131 -
all-7519 -
obs--95.33 %

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