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- PDB-4dwd: Crystal structure of mandelate racemase/muconate lactonizing prot... -

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Basic information

Entry
Database: PDB / ID: 4dwd
TitleCrystal structure of mandelate racemase/muconate lactonizing protein from Paracoccus denitrificans PD1222 complexed with magnesium
ComponentsMandelate racemase/muconate lactonizing enzyme, C-terminal domain protein
KeywordsMETAL BINDING PROTEIN / STRUCTURAL GENOMICS / EFI / Enzyme Function Initiative
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsMalashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of mandelate racemase/muconate lactonizing protein from Paracoccus denitrificans PD1222 complexed with magnesium
Authors: Malashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionFeb 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Structure summary
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)86,00010
Polymers85,7502
Non-polymers2508
Water14,880826
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)343,99940
Polymers342,9988
Non-polymers1,00132
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
Buried area36370 Å2
ΔGint-305 kcal/mol
Surface area85060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.598, 136.598, 80.603
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-501-

MG

21B-501-

MG

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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: 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 826 / 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: 2.19 Å3/Da / Density % sol: 43.9 %
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, soaked for 5 min in 30% PEG400, 0.1M HEPES, pH 7.5, 0.2M MgCl2, 0.1M tartrate, 20% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2010
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. obs: 120795 / % possible obs: 95.5 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.064 / Χ2: 0.917 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.48-1.5110.80.71648880.71178.4
1.51-1.53110.62255230.714188.2
1.53-1.5610.90.55555400.719188.8
1.56-1.5910.80.44656090.748189.7
1.59-1.6310.80.40556520.75190.4
1.63-1.6710.60.34657890.767192.3
1.67-1.7110.50.31359100.775194.1
1.71-1.7510.30.26160000.785196
1.75-1.8110.40.22461260.804197.5
1.81-1.8610.50.17861610.834198.1
1.86-1.9310.50.15761780.953198.4
1.93-2.0110.80.11862690.892199.2
2.01-2.111.20.09562260.883199.3
2.1-2.2111.70.08462850.952199.4
2.21-2.3511.40.08363231.261199.6
2.35-2.5312.60.06463261.119199.7
2.53-2.7912.90.0663851.314199.9
2.79-3.1913.50.04463901.1021100
3.19-4.02120.03264691.046199.7
4.02-5014.20.02667460.831199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 34.75 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å43.2 Å
Translation2.5 Å43.2 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N4E

3n4e


Resolution: 1.5→19.94 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.1656 / WRfactor Rwork: 0.1386 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.913 / SU B: 1.993 / SU ML: 0.035 / SU R Cruickshank DPI: 0.0774 / SU Rfree: 0.0646 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1724 5889 5 %RANDOM
Rwork0.1417 ---
obs0.1433 116924 96.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.74 Å2 / Biso mean: 15.8271 Å2 / Biso min: 6.29 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5569 0 8 826 6403
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195818
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.9747921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5585775
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83823.123253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.28615883
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.891554
X-RAY DIFFRACTIONr_chiral_restr0.0820.2892
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214454
X-RAY DIFFRACTIONr_rigid_bond_restr2.69635818
X-RAY DIFFRACTIONr_sphericity_free14.1915175
X-RAY DIFFRACTIONr_sphericity_bonded5.66256351
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.199 356 -
Rwork0.156 7086 -
all-7442 -
obs--87.71 %
Refinement TLS params.

T11: 0.0085 Å2 / 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 °)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.07150.04240.04580.14050.04650.0844-0.00990.01660.0106-0.01060.0059-0.0025-0.02250.01090.004-0.0026-0.00090.0040.00280.00233.5937-36.43440.5368
20.1211-0.0580.0870.1056-0.01560.1206-0.0087-0.02610.01050.00230.00210.0042-0.022-0.02760.00670.00530.00070.0083-0.00280.0024-18.2398-41.551226.7596
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 374
2X-RAY DIFFRACTION1A500 - 503
3X-RAY DIFFRACTION2B2 - 378
4X-RAY DIFFRACTION2B501 - 504

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