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- PDB-4fq5: Crystal structure of the maleate isomerase Iso(C200A) from Pseudo... -

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Basic information

Entry
Database: PDB / ID: 4fq5
TitleCrystal structure of the maleate isomerase Iso(C200A) from Pseudomonas putida S16 with maleate
ComponentsMaleate cis-trans isomerase
KeywordsISOMERASE / maleate isomerase
Function / homology
Function and homology information


maleate isomerase / maleate isomerase activity
Similarity search - Function
Maleate isomerase / Maleate isomerase/Arylmalonate decarboxylase / Arylmalonate decarboxylase / Rossmann fold - #12500 / : / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MALEIC ACID / Maleate isomerase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsLu, Y. / Chen, D. / Zhang, Z. / Li, Q. / Wu, G. / Xu, P.
CitationJournal: Mol.Microbiol. / Year: 2013
Title: Structural and computational studies of the maleate isomerase from Pseudomonas putida S16 reveal a breathing motion wrapping the substrate inside.
Authors: Chen, D. / Tang, H. / Lu, Y. / Zhang, Z. / Shen, K. / Lin, K. / Zhao, Y.L. / Wu, G. / Xu, P.
History
DepositionJun 25, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Structure summary
Revision 1.2Nov 15, 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 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Maleate cis-trans isomerase
A: Maleate cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3774
Polymers61,1442
Non-polymers2322
Water5,386299
1
B: Maleate cis-trans isomerase
A: Maleate cis-trans isomerase
hetero molecules

B: Maleate cis-trans isomerase
A: Maleate cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,7538
Polymers122,2894
Non-polymers4644
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area8680 Å2
ΔGint-9 kcal/mol
Surface area31760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.725, 66.725, 421.606
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-533-

HOH

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Components

#1: Protein Maleate cis-trans isomerase


Mass: 30572.197 Da / Num. of mol.: 2 / Mutation: C200A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: S16 / Gene: PPS_4060 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F8G0M3
#2: Chemical ChemComp-MAE / MALEIC ACID


Mass: 116.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.22 Å3/Da / Density % sol: 44.48 % / Mosaicity: 0.396 °
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG 3350, 0.1M Tris, pH 8.5, vapor diffusion, hanging drop, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorDetector: CCD / Date: Jan 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 33942 / % possible obs: 99.1 % / Redundancy: 28.2 % / Rmerge(I) obs: 0.081 / Χ2: 0.989 / Net I/σ(I): 11.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.1829.30.40632470.904198.7
2.18-2.2629.20.29332680.923198.8
2.26-2.3729.20.2333031.012199
2.37-2.4929.10.17533031.018199
2.49-2.6528.90.13633301.015199.3
2.65-2.8528.80.10533451.001199.3
2.85-3.1428.50.07933911.007199.5
3.14-3.5928.20.07334381.006199.5
3.59-4.5226.80.06535050.996199.5
4.52-5024.80.04438121.006198.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 5.379 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2414 1714 5.1 %RANDOM
Rwork0.2041 ---
obs0.2059 33869 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.09 Å2 / Biso mean: 32.812 Å2 / Biso min: 14.24 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20.51 Å20 Å2
2--1.02 Å20 Å2
3----1.53 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3729 0 16 299 4044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193797
X-RAY DIFFRACTIONr_angle_refined_deg1.241.9785159
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4025495
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.23422.917144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.8715646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6581536
X-RAY DIFFRACTIONr_chiral_restr0.0880.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212808
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 100 -
Rwork0.236 1995 -
all-2095 -
obs--98.5 %
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)
10.66310.06640.05670.2481-0.02650.90280.01220.00650.0352-0.051-0.0252-0.0068-0.0810.15380.01290.0398-0.00720.00780.13480.01880.0063-12.32628.08116.812
22.09630.3504-0.26120.7644-0.40410.89350.0426-0.1536-0.1235-0.1176-0.00980.08470.2085-0.0639-0.03280.0793-0.0234-0.02260.08270.01290.0234-39.74610.09416.984
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B5 - 254
2X-RAY DIFFRACTION2A6 - 252

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