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- PDB-4u5p: Crystal structure of native RhCC (YP_702633.1) from Rhodococcus j... -

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Basic information

Entry
Database: PDB / ID: 4u5p
TitleCrystal structure of native RhCC (YP_702633.1) from Rhodococcus jostii RHA1 at 1.78 Angstrom
ComponentsRhCC
KeywordsISOMERASE / beta-alpha-beta structural motif / magnesium binding enzyme / tautomerase superfamily
Function / homologyTautomerase, cis-CaaD-like / Putative oxalocrotonate tautomerase enzyme / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta / Tautomerase cis-CaaD-like domain-containing protein
Function and homology information
Biological speciesRhodococcus jostii RHA1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.782 Å
AuthorsPoddar, H. / Rozeboom, H.J. / Thunnissen, A.M.W.H.
Funding support Netherlands, 2items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific ResearchVIDI Grant 700.56.421 Netherlands
European Reserach Council242293
CitationJournal: Biochemistry / Year: 2015
Title: Functional and structural characterization of an unusual cofactor-independent oxygenase.
Authors: Baas, B.J. / Poddar, H. / Geertsema, E.M. / Rozeboom, H.J. / de Vries, M.P. / Permentier, H.P. / Thunnissen, A.M. / Poelarends, G.J.
History
DepositionJul 25, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 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 / pdbx_initial_refinement_model / 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_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.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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_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 / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RhCC
B: RhCC
C: RhCC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9408
Polymers49,9773
Non-polymers9635
Water9,764542
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9230 Å2
ΔGint-21 kcal/mol
Surface area18080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.690, 98.550, 188.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-304-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid
21chain B and segid
31chain C and segid

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segidA0
211chain B and segidB0
311chain C and segidC0
Detailsbiological unit is the same as asym.

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Components

#1: Protein RhCC


Mass: 16658.971 Da / Num. of mol.: 3 / Fragment: UNP Residues 2-142
Source method: isolated from a genetically manipulated source
Details: C-terminal His6-tagged / Source: (gene. exp.) Rhodococcus jostii RHA1 (bacteria) / Gene: RHA1_ro02670 / Plasmid: pET-20b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0SDB1
#2: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / Bis-tris propane


Mass: 282.334 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 542 / 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: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 24-28% PEG 3350, 100mM Bis-tris propane / PH range: 8.0-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 31, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 1.78→94.265 Å / Num. all: 42398 / Num. obs: 42398 / % possible obs: 86.8 % / Redundancy: 3 % / Biso Wilson estimate: 17.89 Å2 / Rpim(I) all: 0.052 / Rrim(I) all: 0.099 / Rsym value: 0.084 / Net I/av σ(I): 5.079 / Net I/σ(I): 7.9 / Num. measured all: 129204
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.78-1.882.90.2572.81836563030.1650.2572.988.7
1.88-1.9930.1644.21803259620.1030.1644.489.6
1.99-2.133.10.1215.41693555370.0750.1215.988.3
2.13-2.33.10.16.41570651440.0620.17.287.5
2.3-2.523.10.096.51443646830.0560.098.486.4
2.52-2.823.10.0767.61301041820.0470.0769.984.7
2.82-3.253.10.0737.61140036240.0440.07311.683.7
3.25-3.983.20.0816.7957630340.0490.08113.681.5
3.98-5.642.90.077.9728424940.0440.0714.186
5.64-46.3523.10.04612.1446014350.0290.04614.186.8

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.9_1692)refinement
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C6V

3c6v


Resolution: 1.782→46.352 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0.85 / Phase error: 18.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1871 3864 5.1 %
Rwork0.1497 71867 -
obs0.1516 42398 80.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.66 Å2 / Biso mean: 22.3283 Å2 / Biso min: 7.57 Å2
Refinement stepCycle: final / Resolution: 1.782→46.352 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3508 0 64 542 4114
Biso mean--40.98 34.05 -
Num. residues----422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083705
X-RAY DIFFRACTIONf_angle_d1.0865032
X-RAY DIFFRACTIONf_chiral_restr0.046521
X-RAY DIFFRACTIONf_plane_restr0.006644
X-RAY DIFFRACTIONf_dihedral_angle_d12.8221481
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2650X-RAY DIFFRACTION5.026TORSIONAL
12B2650X-RAY DIFFRACTION5.026TORSIONAL
13C2650X-RAY DIFFRACTION5.026TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.782-1.80370.26431320.22352544267678
1.8037-1.82660.25151480.21092597274582
1.8266-1.85060.26181440.21132612275684
1.8506-1.8760.24641370.20692648278581
1.876-1.90280.21831550.19562591274684
1.9028-1.93120.20491340.18372646278082
1.9312-1.96130.24981510.17972623277483
1.9613-1.99350.21631620.16562589275182
1.9935-2.02790.20441240.15322618274281
2.0279-2.06470.16981290.15562565269482
2.0647-2.10450.20151210.15432647276881
2.1045-2.14740.1911550.15272560271581
2.1474-2.19410.17981240.14872644276882
2.1941-2.24510.19521460.14932559270580
2.2451-2.30130.20981200.14262610273082
2.3013-2.36350.21290.14312579270880
2.3635-2.4330.18361390.14862558269780
2.433-2.51160.21541520.1482570272281
2.5116-2.60130.22051270.14582547267479
2.6013-2.70550.16341390.14762505264479
2.7055-2.82860.16771600.14162476263678
2.8286-2.97770.19031550.14362498265378
2.9777-3.16420.1921260.14342479260579
3.1642-3.40850.1781400.14522469260977
3.4085-3.75130.15671230.13152398252176
3.7513-4.29380.14311190.12662515263478
4.2938-5.40840.15681380.1252556269481
5.4084-46.36780.19031350.16432664279983

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