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- PDB-1bn5: HUMAN METHIONINE AMINOPEPTIDASE 2 -

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Basic information

Entry
Database: PDB / ID: 1bn5
TitleHUMAN METHIONINE AMINOPEPTIDASE 2
ComponentsMETHIONINE AMINOPEPTIDASE
KeywordsAMINOPEPTIDASE / METHIONINE AMINOPEPTIDASE / HYDROLASE
Function / homology
Function and homology information


N-terminal protein amino acid modification / peptidyl-methionine modification / methionyl aminopeptidase / initiator methionyl aminopeptidase activity / metalloexopeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / protein processing / Inactivation, recovery and regulation of the phototransduction cascade / RNA binding ...N-terminal protein amino acid modification / peptidyl-methionine modification / methionyl aminopeptidase / initiator methionyl aminopeptidase activity / metalloexopeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / protein processing / Inactivation, recovery and regulation of the phototransduction cascade / RNA binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Peptidase M24A, methionine aminopeptidase, subfamily 2 / : / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like ...Peptidase M24A, methionine aminopeptidase, subfamily 2 / : / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / TERTIARY-BUTYL ALCOHOL / Methionine aminopeptidase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLiu, S. / Widom, J. / Kemp, C.W. / Crews, C.M. / Clardy, J.C.
CitationJournal: Science / Year: 1998
Title: Structure of human methionine aminopeptidase-2 complexed with fumagillin.
Authors: Liu, S. / Widom, J. / Kemp, C.W. / Crews, C.M. / Clardy, J.
History
DepositionJul 31, 1998Processing site: BNL
Revision 1.0Jul 31, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: METHIONINE AMINOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2525
Polymers52,9861
Non-polymers2664
Water4,306239
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.490, 99.380, 101.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein METHIONINE AMINOPEPTIDASE


Mass: 52985.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: COMPLEX WITH T-BUTANOL AND COBALT / Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Cell line (production host): SF21 CELLS / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P50579, methionyl aminopeptidase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL


Mass: 74.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 42 %
Crystal growpH: 5.4 / Details: pH 5.4
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.2 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
210 mMHEPES1drop
310 %glycerol1drop
4100 mM1dropNaCl
515-30 %t-butanol1reservoir
633-100 mMsodium citrate1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.922
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 1998 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.922 Å / Relative weight: 1
ReflectionResolution: 1.8→26.5 Å / Num. obs: 42299 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 14.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 6.8 / Rsym value: 0.149 / % possible all: 99.4
Reflection
*PLUS
Num. measured all: 154879

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XGS

1xgs


Resolution: 1.8→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.12 / Details: BULK SOLVENT CORRECTION FROM X-PLOR USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 3019 10 %RANDOM
Rwork0.183 ---
obs-42282 98.4 %-
Displacement parametersBiso mean: 21.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å20 Å2
2--4.042 Å20 Å2
3---3.451 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2780 0 2 249 3031
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0260.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0320.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.742
X-RAY DIFFRACTIONp_mcangle_it2.413
X-RAY DIFFRACTIONp_scbond_it2.552
X-RAY DIFFRACTIONp_scangle_it3.843
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.1740.3
X-RAY DIFFRACTIONp_multtor_nbd0.2410.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1260.03
X-RAY DIFFRACTIONp_planar_tor6.67
X-RAY DIFFRACTIONp_staggered_tor14.115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor26.120
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS

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