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- PDB-2qlw: Crystal structure of rhamnose mutarotase RhaU of Rhizobium legumi... -

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Basic information

Entry
Database: PDB / ID: 2qlw
TitleCrystal structure of rhamnose mutarotase RhaU of Rhizobium leguminosarum
ComponentsRhaU
KeywordsISOMERASE / RhaU / mutarotase / Rhizobium leguminosarum
Function / homology
Function and homology information


L-rhamnose mutarotase / L-rhamnose mutarotase activity / rhamnose catabolic process / cytoplasm
Similarity search - Function
L-rhamnose mutarotase / Rhamnose/fucose mutarotase / L-rhamnose mutarotase / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / L-rhamnose mutarotase
Similarity search - Component
Biological speciesRhizobium leguminosarum bv. trifolii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsCarpena, X. / Loewen, P.C.
CitationJournal: J.Bacteriol. / Year: 2008
Title: RhaU of Rhizobium leguminosarum is a rhamnose mutarotase.
Authors: Richardson, J.S. / Carpena, X. / Switala, J. / Perez-Luque, R. / Donald, L.J. / Loewen, P.C. / Oresnik, I.J.
History
DepositionJul 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RhaU
B: RhaU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,77920
Polymers33,9942
Non-polymers78518
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-35 kcal/mol
Surface area10920 Å2
MethodPISA
2
A: RhaU
B: RhaU
hetero molecules

A: RhaU
B: RhaU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,55740
Polymers67,9874
Non-polymers1,57036
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,x-y,-z1
Buried area13850 Å2
ΔGint-93 kcal/mol
Surface area19670 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)69.241, 69.241, 101.106
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: MSE / End label comp-ID: PHE / Refine code: 6 / Auth seq-ID: 1 - 103 / Label seq-ID: 3 - 105

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein RhaU /


Mass: 16996.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium leguminosarum bv. trifolii (bacteria)
Gene: rhaU / Production host: Escherichia coli (E. coli) / References: UniProt: Q7BSH1
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.72 Å3/Da / Density % sol: 54.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2M Sodium Formate, 0.1M Sodium Acetate pH 4.6, 20% Glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.9079 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 23, 2006 / Details: Mirrors
RadiationMonochromator: SI 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9079 Å / Relative weight: 1
ReflectionRedundancy: 5.7 % / Av σ(I) over netI: 11.2 / Number: 203502 / Rmerge(I) obs: 0.097 / Χ2: 0.95 / D res high: 1.6 Å / D res low: 30 Å / Num. obs: 35978 / % possible obs: 97.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.453088.810.0621.085.1
2.743.4598.710.0640.9535.7
2.392.7498.810.0790.9645.7
2.172.3998.610.090.9675.7
2.022.1798.410.110.9345.7
1.92.029810.1490.915.7
1.81.997.810.2380.9055.7
1.721.897.610.330.9095.8
1.661.7297.310.4490.9575.7
1.61.669710.5890.985.6
ReflectionResolution: 1.6→30 Å / Num. all: 35978 / Num. obs: 35978 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.097 / Χ2: 0.954 / Net I/σ(I): 11.2
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 3.2 / Num. unique all: 3574 / Χ2: 0.98 / % possible all: 97

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT2data extraction
DNAdata collection
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→19.99 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.496 / SU ML: 0.044 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.072 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18 1786 5 %RANDOM
Rwork0.152 ---
all0.153 35783 --
obs0.153 35783 97.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.823 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1748 0 50 220 2018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211946
X-RAY DIFFRACTIONr_bond_other_d0.0070.021322
X-RAY DIFFRACTIONr_angle_refined_deg1.691.9542620
X-RAY DIFFRACTIONr_angle_other_deg1.71133261
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3965226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.34624.30193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07415361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.659159
X-RAY DIFFRACTIONr_chiral_restr0.1360.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022056
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02359
X-RAY DIFFRACTIONr_nbd_refined0.2270.2385
X-RAY DIFFRACTIONr_nbd_other0.2140.21375
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2910
X-RAY DIFFRACTIONr_nbtor_other0.0890.2902
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2149
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.20.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.215
X-RAY DIFFRACTIONr_mcbond_it1.5191.51419
X-RAY DIFFRACTIONr_mcbond_other0.3111.5444
X-RAY DIFFRACTIONr_mcangle_it1.78221849
X-RAY DIFFRACTIONr_scbond_it3.273891
X-RAY DIFFRACTIONr_scangle_it4.5354.5765
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1381 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.465
LOOSE THERMAL1.2610
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 118 -
Rwork0.213 2483 -
obs-2601 96.87 %
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)
10.614-0.0467-0.30860.75120.36070.6761-0.01250.0065-0.07960.0735-0.09040.10760.071-0.09250.1029-0.0185-0.01450.0102-0.0268-0.0235-0.01633.417816.854410.8443
20.606-0.1951-0.01271.0469-0.36940.688-0.00260.10240.0363-0.0275-0.06-0.0715-0.0390.01630.0626-0.02690.0058-0.0111-0.01960.0084-0.031114.588627.0149-5.2807
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 1062 - 108
2X-RAY DIFFRACTION2BB0 - 1062 - 108

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