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- PDB-1qjv: Pectin methylesterase PemA from Erwinia chrysanthemi -

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Basic information

Entry
Database: PDB / ID: 1qjv
TitlePectin methylesterase PemA from Erwinia chrysanthemi
ComponentsPECTIN METHYLESTERASE
KeywordsHYDROLASE (ASPARTYL ESTERASE) / ESTERASE / PECTIN DEGRADATION / RIGHT-HANDED PARALLEL BETA HELIX
Function / homology
Function and homology information


: / pectinesterase / pectinesterase activity / cell wall modification / : / pectin catabolic process / cell outer membrane / extracellular space / extracellular region
Similarity search - Function
: / Pectinesterase, Asp active site / Pectinesterase signature 2. / Pectinesterase, catalytic / Pectinesterase / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Pectinesterase A / Pectinesterase A
Similarity search - Component
Biological speciesERWINIA CHRYSANTHEMI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.37 Å
AuthorsJenkins, J. / Mayans, O. / Smith, D. / Worboys, K. / Pickersgill, R.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Three-Dimensional Structure of Erwinia Chrysanthemi Pectin Methylesterase Reveals a Novel Esterase Active Site
Authors: Jenkins, J. / Mayans, O. / Smith, D. / Worboys, K. / Pickersgill, R.
#1: Journal: Gene / Year: 1993
Title: Characterization and Overexpression of the Pem Gene Encoding Pectin Methylesterase from Erwinia Chrysanthemi Strain-3937
Authors: Laurent, F. / Kotoujansky, A. / Labesse, G. / Bertheau, Y.
#2: Journal: Appl.Microbiol.Biotechnol. / Year: 1991
Title: Production of Pectin Methylesterase from Erwinia Chrysanthemi B374 in Bacillus Subtilis
Authors: Heikinheimo, R. / Hemila, H. / Pakkanen, R. / Palva, I.
#3: Journal: Mol.Microbiol. / Year: 1988
Title: Molecular Cloning and Nucleotide Sequence of the Pectin Methyl Esterase Gene of Erwinia Chrysanthemi B374
Authors: Plastow, G.S.
History
DepositionJul 5, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _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
A: PECTIN METHYLESTERASE
B: PECTIN METHYLESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9984
Polymers73,9282
Non-polymers712
Water11,133618
1
A: PECTIN METHYLESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9992
Polymers36,9641
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PECTIN METHYLESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9992
Polymers36,9641
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.694, 85.507, 96.690
Angle α, β, γ (deg.)90.00, 93.69, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (1, -0.00037, 0.00198), (-0.00036, -0.99997, -0.00781), (0.00199, 0.00781, -0.99997)
Vector: -3.11715, -32.05247, 48.21067)
DetailsBIOLOGICAL_UNIT: MONOMER

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Components

#1: Protein PECTIN METHYLESTERASE / PECTINESTERASE


Mass: 36963.773 Da / Num. of mol.: 2 / Fragment: MATURE ENZYME (RESIDUES 25-366)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ERWINIA CHRYSANTHEMI (bacteria) / Strain: B374
Description: THE EXPRESSION SYSTEM STRAIN IS FROM THE UK NATIONAL COLLECTION OF PLANT PATHOGENIC BACTERIA (NCPPB)
Cellular location: EXTRACELLULAR / Gene: PEMA / Plasmid: PKTH1746 / Cellular location (production host): SECRETED / Gene (production host): ALPHA AMYLASE PROMOTER / Production host: BACILLUS SUBTILIS (bacteria) / Strain (production host): IHO 6064 (SACA321, METB5)
References: UniProt: P07863, UniProt: P0C1A8*PLUS, pectinesterase
#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 618 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSTRAIN B374 BUT HISTIDINE 80 AS IN STRAIN 3937 COORDINATES START AT ALA 25 AFTER LEADER SEQUENCE

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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: 2.8 Å3/Da / Density % sol: 50 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: HANGING DROP AGAINST 2.0 M AMMONIUM SULFATE AND 0.1M MES BUFFER AT PH 6.8 THE PROTEIN CONCENTATION WAS ABOUT 3 MG./ML.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.6 Mammonium sulfate1drop
20.1 MMES1drop
32.0 Mammonium sulfate1reservoir
40.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9058
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 27, 1998 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9058 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 32934 / % possible obs: 99 % / Redundancy: 4.04 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.43
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.04 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 3 / % possible all: 82.3
Reflection
*PLUS
% possible obs: 99.1 %
Reflection shell
*PLUS
% possible obs: 82.6 % / Rmerge(I) obs: 0.224

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Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.5phasing
RefinementMethod to determine structure: MIR / Resolution: 2.37→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 138672009.62 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: IN EACH PROTEIN CHAIN RESIDUE CYS 192 WAS FOUND TO HAVE TWO DIFFERENT CONFORMATIONS WITH EQUAL OCCUPANCIES THAT ARE ESSENTIALLY RELATED BY A 120 DEG. ROTATION ABOUT CHI1. THE CYS 192 IN EACH ...Details: IN EACH PROTEIN CHAIN RESIDUE CYS 192 WAS FOUND TO HAVE TWO DIFFERENT CONFORMATIONS WITH EQUAL OCCUPANCIES THAT ARE ESSENTIALLY RELATED BY A 120 DEG. ROTATION ABOUT CHI1. THE CYS 192 IN EACH CHAIN WITH ALTCODE B FORMS A DISULFIDE TO CYS 212. THE RESIDUE CYS 212 HAS ALMOST THE SAME CONFORMATION WITH AND WITHOUT THE DISULFIDE.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1346 4.1 %RANDOM
Rwork0.17 ---
obs0.17 32857 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.2648 Å2 / ksol: 0.383205 e/Å3
Displacement parametersBiso mean: 17.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.37 Å20 Å20.83 Å2
2--0.04 Å20 Å2
3---2.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.37→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5214 0 2 618 5834
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.631.5
X-RAY DIFFRACTIONc_mcangle_it3.52
X-RAY DIFFRACTIONc_scbond_it4.612
X-RAY DIFFRACTIONc_scangle_it5.472.5
Refine LS restraints NCSRms dev Biso : 0.701 Å2 / Rms dev position: 0.0243 Å / Weight Biso : 0.5 / Weight position: 400
LS refinement shellResolution: 2.37→2.52 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.248 217 4.4 %
Rwork0.195 4701 -
obs--88.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.23
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.06

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