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- PDB-3n4e: CRYSTAL STRUCTURE OF mandelate racemase/muconate lactonizing prot... -

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Basic information

Entry
Database: PDB / ID: 3n4e
TitleCRYSTAL STRUCTURE OF mandelate racemase/muconate lactonizing protein from Paracoccus denitrificans Pd1222
ComponentsMandelate racemase/muconate lactonizing enzyme, C-terminal domain protein
KeywordsISOMERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / enolase / PSI-2 / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


hydro-lyase activity / carbohydrate catabolic process / magnesium ion binding
Similarity search - Function
: / 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/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
Mandelate racemase/muconate lactonizing enzyme, C-terminal domain protein
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsMalashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF mandelate racemase/muconate lactonizing protein from Paracoccus denitrificans Pd1222
Authors: Malashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionMay 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 21, 2018Group: Data collection / Derived calculations / Structure summary
Category: audit_author / pdbx_struct_special_symmetry / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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_auth_seq_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.pdbx_leaving_atom_flag / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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, C-terminal domain protein
B: Mandelate racemase/muconate lactonizing enzyme, C-terminal domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,06110
Polymers85,7502
Non-polymers3118
Water6,557364
1
A: Mandelate racemase/muconate lactonizing enzyme, C-terminal domain protein
B: Mandelate racemase/muconate lactonizing enzyme, C-terminal domain protein
hetero molecules

A: Mandelate racemase/muconate lactonizing enzyme, C-terminal domain protein
B: Mandelate racemase/muconate lactonizing enzyme, C-terminal domain protein
hetero molecules

A: Mandelate racemase/muconate lactonizing enzyme, C-terminal domain protein
B: Mandelate racemase/muconate lactonizing enzyme, C-terminal domain protein
hetero molecules

A: Mandelate racemase/muconate lactonizing enzyme, C-terminal domain protein
B: Mandelate racemase/muconate lactonizing enzyme, C-terminal domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)344,24440
Polymers342,9988
Non-polymers1,24532
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area35610 Å2
ΔGint-279 kcal/mol
Surface area83670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.711, 137.711, 80.363
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-502-

CA

21A-503-

CL

31B-501-

CA

41B-503-

CL

51B-522-

HOH

Detailsoctamer

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Components

#1: Protein Mandelate racemase/muconate lactonizing enzyme, C-terminal domain protein


Mass: 42874.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: PD1222 / Gene: 69934097, Pden_0244 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: A1AYL4
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.22 Å3/Da / Density % sol: 44.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 28% PEG 400, 0.1 M Na-HEPES, 0.2 M Ca chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionRedundancy: 6.9 % / Av σ(I) over netI: 15.04 / Number: 397774 / Rmerge(I) obs: 0.18 / Χ2: 1.58 / D res high: 2.4 Å / D res low: 50 Å / Num. obs: 57793 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.515099.910.0671.7897.8
5.176.5110010.091.2967.5
4.525.1710010.0891.7047.5
4.14.5210010.1052.0147.5
3.814.110010.1221.9837.5
3.583.8110010.1351.7587.4
3.413.5810010.1651.6077.2
3.263.4110010.1961.5177
3.133.2610010.2381.4736.9
3.023.1310010.271.456.8
2.933.0210010.3121.3666.7
2.852.9310010.3461.4416.6
2.772.8510010.4081.3716.6
2.72.7710010.4561.4446.5
2.642.710010.4871.4626.5
2.592.6410010.5531.4646.4
2.532.5910010.631.4066.4
2.492.5310010.6841.5596.3
2.442.4910010.7051.5826.3
2.42.4410010.751.6176.3
ReflectionResolution: 2.4→50 Å / Num. obs: 57793 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 5.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.4-2.446.30.75100
2.44-2.496.30.705100
2.49-2.536.30.684100
2.53-2.596.40.63100
2.59-2.646.40.553100
2.64-2.76.50.487100
2.7-2.776.50.456100
2.77-2.856.60.408100
2.85-2.936.60.346100
2.93-3.026.70.312100
3.02-3.136.80.27100
3.13-3.266.90.238100
3.26-3.4170.196100
3.41-3.587.20.165100
3.58-3.817.40.135100
3.81-4.17.50.122100
4.1-4.527.50.105100
4.52-5.177.50.089100
5.17-6.517.50.09100
6.51-507.80.06799.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→19.93 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 14.743 / SU ML: 0.155 / SU R Cruickshank DPI: 0.4 / Cross valid method: THROUGHOUT / ESU R: 0.405 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21266 1542 5 %RANDOM
Rwork0.15748 ---
obs0.16031 28998 99.36 %-
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: 25.641 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5517 0 8 364 5889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225647
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2611.967665
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6485737
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69323.08237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22615918
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2291551
X-RAY DIFFRACTIONr_chiral_restr0.0850.2868
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214283
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_it0.7593.53634
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.242505800
X-RAY DIFFRACTIONr_scbond_it8.297502013
X-RAY DIFFRACTIONr_scangle_it0.9864.51862
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 92 -
Rwork0.179 2084 -
obs--98.11 %
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)
10.5367-0.0649-0.11560.43380.10570.2991-0.00620.04410.0363-0.0410.01410.0741-0.002-0.0052-0.00790.0162-0.0052-0.01330.01850.01170.021237.32414.71620.8049
20.42380.17150.09820.48270.20240.32950.0047-0.0517-0.03470.0385-0.00560.03760.0183-0.02970.00090.01450.00280.00720.03190.01450.012741.7487-16.960526.9792
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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