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- PDB-2h4q: Crystal structure of a M-loop deletion variant of MENT in the cle... -

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Basic information

Entry
Database: PDB / ID: 2h4q
TitleCrystal structure of a M-loop deletion variant of MENT in the cleaved conformation
Components(Heterochromatin-associated protein MENT) x 2
KeywordsHYDROLASE INHIBITOR / Serine protease inhibitor / Serpin
Function / homology
Function and homology information


nucleate erythrocyte maturation / chromosome condensation / serine-type endopeptidase inhibitor activity / chromatin DNA binding / chromatin organization / chromatin / extracellular space / nucleoplasm
Similarity search - Function
Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) ...Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Heterochromatin-associated protein MENT
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWhisstock, J.C. / Buckle, A.M. / McGowan, S. / Irving, J.A.
CitationJournal: Embo J. / Year: 2006
Title: X-ray crystal structure of MENT: evidence for functional loop-sheet polymers in chromatin condensation.
Authors: McGowan, S. / Buckle, A.M. / Irving, J.A. / Ong, P.C. / Bashtannyk-Puhalovich, T.A. / Kan, W.T. / Henderson, K.N. / Bulynko, Y.A. / Popova, E.Y. / Smith, A.I. / Bottomley, S.P. / Rossjohn, J. ...Authors: McGowan, S. / Buckle, A.M. / Irving, J.A. / Ong, P.C. / Bashtannyk-Puhalovich, T.A. / Kan, W.T. / Henderson, K.N. / Bulynko, Y.A. / Popova, E.Y. / Smith, A.I. / Bottomley, S.P. / Rossjohn, J. / Grigoryev, S.A. / Pike, R.N. / Whisstock, J.C.
History
DepositionMay 25, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heterochromatin-associated protein MENT
B: Heterochromatin-associated protein MENT


Theoretical massNumber of molelcules
Total (without water)48,1392
Polymers48,1392
Non-polymers00
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-37 kcal/mol
Surface area16580 Å2
MethodPISA
2
A: Heterochromatin-associated protein MENT
B: Heterochromatin-associated protein MENT
x 6


Theoretical massNumber of molelcules
Total (without water)288,83512
Polymers288,83512
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area46740 Å2
ΔGint-255 kcal/mol
Surface area81500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.194, 150.194, 175.485
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-370-

HOH

21A-427-

HOH

31A-556-

HOH

41A-679-

HOH

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Components

#1: Protein Heterochromatin-associated protein MENT / MENT


Mass: 43953.160 Da / Num. of mol.: 1 / Fragment: residues 1-369 / Mutation: A361V, deletion mutant(residues 61-88)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: ment-1 / Plasmid: pBAD-HisA / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: O73790
#2: Protein/peptide Heterochromatin-associated protein MENT / MENT


Mass: 4186.003 Da / Num. of mol.: 1 / Fragment: residues 377-409
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: ment-1 / Plasmid: pBAD-HisA / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: O73790
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 3.97 Å3/Da / Density % sol: 68.99 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M sodium acetate, 12-15% PEG 8000, pH 5.5-6.5, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5148 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 7, 2003 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5148 Å / Relative weight: 1
ReflectionAv σ(I) over netI: 14.4 / Number: 151605 / Rmerge(I) obs: 0.062 / Χ2: 1.25 / D res high: 2.1 Å / D res low: 50 Å / Num. obs: 44120 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
4.525094.910.0211.142
3.594.5299.410.0251.145
3.143.5999.810.0421.26
2.853.1499.910.0821.291
2.652.8599.910.1361.287
2.492.6510010.191.237
2.372.4999.910.2691.234
2.262.3799.910.341.278
2.182.2699.910.4531.305
2.12.1810010.5871.288
ReflectionResolution: 2.1→105.4 Å / Num. all: 44451 / Num. obs: 44451 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 20.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 2.4 / % possible all: 94.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
CrystalClear(MSC/RIGAKU)data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QLP

1qlp


Resolution: 2.1→24.35 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.437 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1782 4 %RANDOM
Rwork0.188 ---
all0.189 44118 --
obs0.189 44118 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.052 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å2-0.35 Å20 Å2
2---0.7 Å20 Å2
3---1.06 Å2
Refinement stepCycle: LAST / Resolution: 2.1→24.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3093 0 0 350 3443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0223164
X-RAY DIFFRACTIONr_bond_other_d0.0010.022880
X-RAY DIFFRACTIONr_angle_refined_deg0.8741.9554264
X-RAY DIFFRACTIONr_angle_other_deg0.66236710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6455383
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.24324.071140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.18615583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1321519
X-RAY DIFFRACTIONr_chiral_restr0.0520.2480
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023439
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02648
X-RAY DIFFRACTIONr_nbd_refined0.1770.2600
X-RAY DIFFRACTIONr_nbd_other0.1550.22928
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21528
X-RAY DIFFRACTIONr_nbtor_other0.0770.21789
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2314
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1470.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.230
X-RAY DIFFRACTIONr_mcbond_it0.86232030
X-RAY DIFFRACTIONr_mcbond_other0.1233771
X-RAY DIFFRACTIONr_mcangle_it1.37653124
X-RAY DIFFRACTIONr_scbond_it1.88171334
X-RAY DIFFRACTIONr_scangle_it2.838101140
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 126 -
Rwork0.274 3104 -
obs-3230 99.57 %

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