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- PDB-4fq7: Crystal structure of the maleate isomerase Iso from Pseudomonas p... -

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Basic information

Entry
Database: PDB / ID: 4fq7
TitleCrystal structure of the maleate isomerase Iso from Pseudomonas putida S16
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
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,2092
Polymers61,2092
Non-polymers00
Water21612
1
A: Maleate cis-trans isomerase
B: Maleate cis-trans isomerase

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


Theoretical massNumber of molelcules
Total (without water)122,4174
Polymers122,4174
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area7970 Å2
ΔGint-17 kcal/mol
Surface area33140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.469, 66.469, 413.839
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 4 / Auth seq-ID: 10 - 250 / Label seq-ID: 31 - 271

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Maleate cis-trans isomerase


Mass: 30604.260 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.16 Å3/Da / Density % sol: 42.94 % / Mosaicity: 0.776 °
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.4M (NH4)2SO4, 120mM NaCl, 0.1M HEPES, pH 7.5, 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, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 43048 / % possible obs: 99.9 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.074 / Χ2: 1 / Net I/σ(I): 11.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.95-3.0610.80.43643000.9991100
3.06-3.1810.80.36343511.0011100
3.18-3.3210.80.24343500.9921100
3.32-3.510.80.16742871.0071100
3.5-3.7210.90.12342651.0041100
3.72-410.80.142480.994199.9
4-4.4110.70.083437011100
4.41-5.0410.50.06442830.998199.8
5.04-6.3510.70.0542800.997199.9
6.35-5010.60.0343141.006199.3

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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: 3→50 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.827 / Occupancy max: 1 / Occupancy min: 1 / SU B: 43.055 / SU ML: 0.348 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3005 575 4.9 %RANDOM
Rwork0.2406 ---
obs0.2437 11851 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.55 Å2 / Biso mean: 56.6601 Å2 / Biso min: 23.11 Å2
Baniso -1Baniso -2Baniso -3
1-2.97 Å20 Å20 Å2
2--2.97 Å20 Å2
3----5.94 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3720 0 0 12 3732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0193772
X-RAY DIFFRACTIONr_angle_refined_deg1.0371.9765124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.115494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.96822.958142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.96515654
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5461536
X-RAY DIFFRACTIONr_chiral_restr0.070.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212764
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1809 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.320.5
MEDIUM THERMAL3.182
LS refinement shellResolution: 2.998→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.469 38 -
Rwork0.327 783 -
all-821 -
obs--96.7 %
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)
14.0615-0.4409-0.01571.64470.06882.97250.0083-0.40210.01630.2464-0.01080.1159-0.2534-0.23370.00240.0620.01180.0230.060400.077124.9373-9.4639-16.3289
23.3297-0.88960.14541.9679-0.04733.1227-0.0528-0.37320.24350.34390.0575-0.2537-0.02850.5318-0.00480.06990.0183-0.01530.24170.07560.138252.13-27.114-16.2108
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 252
2X-RAY DIFFRACTION2B5 - 252

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