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- PDB-3rcy: CRYSTAL STRUCTURE OF Mandelate racemase/muconate lactonizing enzy... -

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Entry
Database: PDB / ID: 3rcy
TitleCRYSTAL STRUCTURE OF Mandelate racemase/muconate lactonizing enzyme-like protein from Roseovarius sp. TM1035
ComponentsMandelate racemase/muconate lactonizing enzyme-like protein
KeywordsISOMERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMICS RESEARCH CONSORTIUM / NYSGRC / PSI-Biology
Function / homology
Function and homology information


Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal ...Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-D-ribofuranose / Mandelate racemase/muconate lactonizing enzyme-like protein
Similarity search - Component
Biological speciesRoseovarius sp. TM1035 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.994 Å
AuthorsMalashkevich, V.N. / Toro, R. / Seidel, R. / Garrett, S. / Foti, R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF Mandelate racemase/muconate lactonizing enzyme-like protein from Roseovarius sp. TM1035
Authors: Malashkevich, V.N. / Toro, R. / Seidel, R. / Garrett, S. / Foti, R. / Almo, S.C.
History
DepositionMar 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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 / _pdbx_validate_chiral.auth_atom_id / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mandelate racemase/muconate lactonizing enzyme-like protein
B: Mandelate racemase/muconate lactonizing enzyme-like protein
C: Mandelate racemase/muconate lactonizing enzyme-like protein
D: Mandelate racemase/muconate lactonizing enzyme-like protein
E: Mandelate racemase/muconate lactonizing enzyme-like protein
F: Mandelate racemase/muconate lactonizing enzyme-like protein
G: Mandelate racemase/muconate lactonizing enzyme-like protein
H: Mandelate racemase/muconate lactonizing enzyme-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)380,56142
Polymers377,5088
Non-polymers3,05334
Water41,4892303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area51910 Å2
ΔGint-228 kcal/mol
Surface area77430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.978, 162.143, 141.954
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21A
31B
41C
51E
61F
71G
81H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111D-99999 - 99999
2111A-99999 - 99999
3111B-99999 - 99999
4111C-99999 - 99999
5111E-99999 - 99999
6111F-99999 - 99999
7111G-99999 - 99999
8111H-99999 - 99999
Detailsoctamer

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Components

#1: Protein
Mandelate racemase/muconate lactonizing enzyme-like protein


Mass: 47188.531 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Roseovarius sp. TM1035 (bacteria) / Strain: TM1035 / Gene: 149202287, RTM1035_13208 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: A6DZ31
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#4: Sugar
ChemComp-RIB / alpha-D-ribofuranose / alpha-D-ribose / D-ribose / ribose / Ribose


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DRibfaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-ribofuranoseCOMMON NAMEGMML 1.0
a-D-RibfIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2303 / 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: 44.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.072 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 226795 / % possible obs: 99.5 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 6.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.99-2.027.10.75189.2
2.02-2.067.40.6211100
2.06-2.17.40.5691100
2.1-2.147.40.5061100
2.14-2.197.50.4351100
2.19-2.247.50.4081100
2.24-2.37.50.3711100
2.3-2.367.50.3221100
2.36-2.437.50.3061100
2.43-2.517.50.2651100
2.51-2.67.50.2461100
2.6-2.77.50.2121100
2.7-2.827.50.1881100
2.82-2.977.40.161100
2.97-3.167.40.1331100
3.16-3.47.40.1121100
3.4-3.747.20.0951100
3.74-4.297.10.0831100
4.29-5.46.90.0731100
5.4-507.10.069199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2OX4
Resolution: 1.994→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.771 / SU ML: 0.085 / SU R Cruickshank DPI: 0.1488 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1809 11321 5 %RANDOM
Rwork0.14688 ---
obs0.14856 214614 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.222 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.994→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24122 0 196 2303 26621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02225179
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1141.96534355
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.67253223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38422.7791047
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.051153772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.26815194
X-RAY DIFFRACTIONr_chiral_restr0.0720.23715
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02219494
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4843.515863
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8785025436
X-RAY DIFFRACTIONr_scbond_it4.482509316
X-RAY DIFFRACTIONr_scangle_it0.5424.58886
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2945 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Dtight positional0.185
Atight positional0.165
Btight positional0.135
Ctight positional0.195
Etight positional0.165
Ftight positional0.165
Gtight positional0.145
Htight positional0.145
Dtight thermal1.7910
Atight thermal1.910
Btight thermal1.6510
Ctight thermal1.9110
Etight thermal2.1710
Ftight thermal1.5410
Gtight thermal1.7510
Htight thermal1.3510
LS refinement shellResolution: 1.994→2.045 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 815 -
Rwork0.204 15453 -
obs--98.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.27040.0377-0.01320.2406-0.01250.2087-0.02290.00590.0339-0.06220.01230.0354-0.0193-0.03480.01060.05830.001-0.02110.00940.00960.041518.252455.94828.4735
20.35460.0194-0.05320.34810.01980.2395-0.0245-0.031-0.094-0.02460.00180.02630.0737-0.03510.02270.0728-0.00790.01440.01450.02190.07219.78313.715620.6816
30.2521-0.06410.00740.3127-0.04890.2399-0.0069-0.03740.0631-0.02840.006-0.0549-0.05330.0480.00090.0434-0.0139-0.00270.0168-0.00490.054646.813970.709422.4734
40.25280.0027-0.00030.20990.03860.2829-0.0293-0.0047-0.0406-0.06340.0108-0.03830.02320.04360.01850.05710.00370.03050.00870.01020.049148.314529.30296.6571
50.26370.0027-0.04040.25760.00580.2225-0.0212-0.09550.05340.02110.02170.0282-0.042-0.0258-0.00050.01670.0231-0.0050.0509-0.02030.014718.105568.64450.5059
60.3942-0.01110.00090.22980.08770.2603-0.0099-0.163-0.06090.0459-0.01050.0260.0525-0.0060.02040.04380.00940.01570.12880.0560.030319.677926.246162.7708
70.26140.01970.00930.204-0.01280.2058-0.018-0.14740.02590.0476-0.0022-0.0506-0.01590.04430.02030.02280.0128-0.01930.142-0.00670.020347.980554.893963.6065
80.37260.0799-0.03880.34790.05750.2633-0.0153-0.1473-0.11390.04840.0076-0.07340.08570.07040.00760.06180.0420.00460.10140.07240.082449.089113.668347.7838
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999
5X-RAY DIFFRACTION5E-10 - 9999
6X-RAY DIFFRACTION6F-10 - 9999
7X-RAY DIFFRACTION7G-10 - 9999
8X-RAY DIFFRACTION8H-10 - 9999

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