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- PDB-1qlm: The crystal structure of methenyltetrahydromethanopterin cyclohyd... -

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Basic information

Entry
Database: PDB / ID: 1qlm
TitleThe crystal structure of methenyltetrahydromethanopterin cyclohydrolase from the hyperthermophilic archaeon Methanopyrus kandleri
ComponentsMETHENYLTETRAHYDROMETHANOPTERIN CYCLOHYDROLASE
KeywordsHYDROLASE / METHANOGENESIS / BIOLOGICAL METHANOGENESIS / TETRAHYDROMETHANOPTERIN
Function / homology
Function and homology information


methenyltetrahydromethanopterin cyclohydrolase / methenyltetrahydromethanopterin cyclohydrolase activity / methanogenesis, from carbon dioxide / one-carbon metabolic process / cytoplasm
Similarity search - Function
Methenyltetrahydromethanopterin Cyclohydrolase; Chain A, domain 1 / Methenyltetrahydromethanopterin Cyclohydrolase; Chain A, domain 1 / Methenyltetrahydromethanopterin Cyclohydrolase; Chain A, domain 2 / Methenyltetrahydromethanopterin Cyclohydrolase; Chain A, domain 2 / Methenyltetrahydromethanopterin cyclohydrolase / Cyclohydrolase (MCH) / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Methenyltetrahydromethanopterin cyclohydrolase
Similarity search - Component
Biological speciesMETHANOPYRUS KANDLERI (archaea)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2 Å
AuthorsGrabarse, W.
CitationJournal: Structure / Year: 1999
Title: The Crystal Structure of Methenyltetrahydromethano- Pterin Cyclohydrolase from the Hyperthermophilic Archaeon Methanopyrus Kandleri
Authors: Grabarse, W. / Vaupel, M. / Vorholt, J.A. / Shima, S. / Thauer, R.K. / Wittershagen, A. / Bourenkov, G. / Bartunik, H.D. / Ermler, U.
History
DepositionSep 1, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 1999Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: METHENYLTETRAHYDROMETHANOPTERIN CYCLOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3794
Polymers34,0941
Non-polymers2853
Water3,855214
1
A: METHENYLTETRAHYDROMETHANOPTERIN CYCLOHYDROLASE
hetero molecules

A: METHENYLTETRAHYDROMETHANOPTERIN CYCLOHYDROLASE
hetero molecules

A: METHENYLTETRAHYDROMETHANOPTERIN CYCLOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,13612
Polymers102,2823
Non-polymers8559
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area7830 Å2
ΔGint-80.6 kcal/mol
Surface area32040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.900, 125.900, 172.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein METHENYLTETRAHYDROMETHANOPTERIN CYCLOHYDROLASE / / METHENYL-H4MPT CYCLOHYDROLASE


Mass: 34093.875 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: THREE PHOSPHATE MOLECULES / Source: (gene. exp.) METHANOPYRUS KANDLERI (archaea) / Description: HETEROLOGOUSLY EXPRESSED IN ESCHERICHIA COLI / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P94954, methenyltetrahydromethanopterin cyclohydrolase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSER A 315, HETEROLOGOUS EXPRESSION

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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 % sol: 76 %
Crystal growpH: 4 / Details: pH 4.00
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
250 mMTris-HCl1drop
328 %PEG10001reservoir
430 %glycerol1reservoir
50.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: R-AXIS IIC / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 54396 / % possible obs: 98.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.081 / Net I/σ(I): 10.3
Reflection shellResolution: 2→2.13 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.31 / % possible all: 98.7
Reflection shell
*PLUS
% possible obs: 98.7 %

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Processing

Software
NameVersionClassification
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.3phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2→30 Å / Rfactor Rfree error: 0.004 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2758 5.1 %RANDOM
Rwork0.198 ---
obs0.198 54396 98.7 %-
Displacement parametersBiso mean: 26.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.1 Å2-2.01 Å20 Å2
2---2.16 Å20 Å2
3---4.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 15 214 2621
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg0.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.27
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.731.5
X-RAY DIFFRACTIONc_mcangle_it1.282
X-RAY DIFFRACTIONc_scbond_it1.232
X-RAY DIFFRACTIONc_scangle_it1.982.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.26 473 5.3 %
Rwork0.253 8371 -
obs--98.7 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.27

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