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- PDB-1o0x: Crystal structure of Methionine aminopeptidase (TM1478) from Ther... -

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Basic information

Entry
Database: PDB / ID: 1o0x
TitleCrystal structure of Methionine aminopeptidase (TM1478) from Thermotoga maritima at 1.90 A resolution
ComponentsMethionine aminopeptidase
KeywordsHYDROLASE / TM1478 / Methionine aminopeptidase / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information


: / methionyl aminopeptidase / metalloaminopeptidase activity / metal ion binding
Similarity search - Function
Methionine aminopeptidase subfamily 1 signature. / Peptidase M24A, methionine aminopeptidase, subfamily 1 / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Methionine aminopeptidase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT WITH PROGRAM AMORE / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of a methionine aminopeptidase (TM1478) from Thermotoga maritima at 1.9 A resolution.
Authors: Spraggon, G. / Schwarzenbacher, R. / Kreusch, A. / McMullan, D. / Brinen, L.S. / Canaves, J.M. / Dai, X. / Deacon, A.M. / Elsliger, M.A. / Eshagi, S. / Floyd, R. / Godzik, A. / Grittini, C. ...Authors: Spraggon, G. / Schwarzenbacher, R. / Kreusch, A. / McMullan, D. / Brinen, L.S. / Canaves, J.M. / Dai, X. / Deacon, A.M. / Elsliger, M.A. / Eshagi, S. / Floyd, R. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Jaroszewski, L. / Karlak, C. / Klock, H.E. / Koesema, E. / Kovarik, J.S. / Kuhn, P. / McPhillips, T.M. / Miller, M.D. / Morse, A. / Moy, K. / Ouyang, J. / Page, R. / Quijano, K. / Rezezadeh, F. / Robb, A. / Sims, E. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / Vincent, J. / von Delft, F. / Wang, X. / West, B. / Wolf, G. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Lesley, S.A. / Wilson, I.A.
History
DepositionSep 13, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.5Jan 25, 2023Group: 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 1.6Sep 20, 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

Downloads & links

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Assembly

Deposited unit
A: Methionine aminopeptidase


Theoretical massNumber of molelcules
Total (without water)28,9921
Polymers28,9921
Non-polymers00
Water3,513195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.580, 62.580, 146.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Methionine aminopeptidase


Mass: 28991.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1478 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1I7, methionyl aminopeptidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 293 K / pH: 5.6
Details: 19% iso-propanol, 19% P4K, 0.095 M Na-citrate pH 5.6, 5% glycerol, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K, pH 5.60
Crystal grow
*PLUS
pH: 7.9 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris1droppH7.9
2150 mM1dropNaCl
30.25 mMTCEP1drop
410 mg/mlprotein1drop
519 %isopropanol1reservoir
619 %PEG40001reservoir
70.095 Msodium citrate1reservoirpH5.6
85 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 29, 2001
RadiationMonochromator: ASYMMETRICALLY CUT SI CRYSTAL, CYLINDRICALLY BENT
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 21470 / % possible obs: 90.6 % / Biso Wilson estimate: 53 Å2 / Rsym value: 0.07 / Net I/σ(I): 16.53
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 2.95 / % possible all: 90
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 50 Å / Num. measured all: 102128 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 90 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOSFLMdata reduction
CCP4data reduction
SCALEPACKdata scaling
SnBphasing
MLPHAREphasing
CCP4model building
SOLVEphasing
CNS1refinement
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT WITH PROGRAM AMORE
Starting model: 1MAT

1mat


Resolution: 1.9→47.53 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: FREE R / σ(F): 0
Stereochemistry target values: STANDARD CNS DICTIONARY/ENGH AND HUBER
Details: ASN 77 IS IN DISALLOWED REGION OF RAMACHANDRAN. THIS IS NOT PART OF THE ACTIVE SITE BUT IS A CONSERVED FEATURE OF ALL METHIONINE AMINO PEPTIDASES. A DIMETAL BINDING SITE LOCATED AT THE ...Details: ASN 77 IS IN DISALLOWED REGION OF RAMACHANDRAN. THIS IS NOT PART OF THE ACTIVE SITE BUT IS A CONSERVED FEATURE OF ALL METHIONINE AMINO PEPTIDASES. A DIMETAL BINDING SITE LOCATED AT THE ACTIVE SITE OF THE MOLECULE DOES NOT HAVE ANY METALS BOUND. HIS 174 HAS A CLEARLY DEFINED DOUBLE CONFORMATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1098 4.6 %RANDOM
Rwork0.203 ---
obs0.203 21420 90.3 %-
Solvent computationSolvent model: BULK SOLVENT CORRECTION / Bsol: 0.4 Å2 / ksol: 76.77 e/Å3
Displacement parametersBiso mean: 44.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.278 Å20 Å20 Å2
2---4.288 Å20 Å2
3---5.566 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.9→47.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1934 0 0 195 2129
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
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_deg1.99
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.3551.5
X-RAY DIFFRACTIONc_mcangle_it3.9982
X-RAY DIFFRACTIONc_scbond_it5.3772
X-RAY DIFFRACTIONc_scangle_it7.1942.5
LS refinement shellResolution: 1.9→1.93 Å / Total num. of bins used: 21
RfactorNum. reflection% reflection
Rfree0.5043 53 5.8 %
Rwork0.4106 855 -
Software
*PLUS
Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.47

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