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- PDB-1b6a: HUMAN METHIONINE AMINOPEPTIDASE 2 COMPLEXED WITH TNP-470 -

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Basic information

Entry
Database: PDB / ID: 1b6a
TitleHUMAN METHIONINE AMINOPEPTIDASE 2 COMPLEXED WITH TNP-470
ComponentsMETHIONINE AMINOPEPTIDASEMethionyl aminopeptidase
KeywordsANGIOGENESIS INHIBITOR / AMINOPEPTIDASE
Function / homology
Function and homology information


N-terminal protein amino acid modification / peptidyl-methionine modification / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / 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 / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / 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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...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
: / Chem-TN4 / Methionine aminopeptidase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsLiu, S. / 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
DepositionJan 13, 1999Processing site: BNL
Revision 1.0Jan 13, 2000Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 31, 2011Group: Non-polymer description
Revision 1.4Nov 20, 2019Group: Advisory / Derived calculations
Category: database_PDB_caveat / pdbx_struct_conn_angle / struct_conn
Revision 1.5Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / 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_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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: METHIONINE AMINOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4934
Polymers52,9721
Non-polymers5223
Water3,837213
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.558, 99.060, 101.508
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 / Methionyl aminopeptidase


Mass: 52971.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: TNP-470 COVALENTLY LINKED TO HIS 231 NE2 / Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Genus (production host): Nucleopolyhedrovirus / Cell line (production host): SF21 / Production host: Spodoptera frugiperda MNPV (virus) / 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-TN4 / (1R,2S,3S,4R)-4-hydroxy-2-methoxy-4-methyl-3-[(2R,3R)-2-methyl-3-(3-methylbut-2-en-1-yl)oxiran-2-yl]cyclohexyl (chloroacetyl)carbamate / TNP-470 (Open form)


Mass: 403.898 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H30ClNO6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growpH: 5.4 / Details: pH 5.40
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.979
DetectorType: ADSC / Detector: CCD / Date: Aug 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→25 Å / Num. obs: 59207 / % possible obs: 96 % / Redundancy: 4 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 11.7
Reflection shellResolution: 1.58→1.67 Å / Redundancy: 3 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 4.3 / Rsym value: 0.231 / % possible all: 85.8
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 25 Å / Redundancy: 4 %
Reflection shell
*PLUS
Redundancy: 3 % / Mean I/σ(I) obs: 4.3

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Processing

Software
NameVersionClassification
SYNCHROTRONdata collection
SCALAdata scaling
CNS0.4refinement
SOFTWAREAT SYNCHROTRONdata reduction
CCP4(SCALA)data scaling
CNS0.4phasing
RefinementStarting model: PDB ENTRY 1BN5

1bn5


Resolution: 1.6→6 Å / Rfactor Rfree error: 0.004 / Data cutoff high rms absF: 2167549.47 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2935 5.1 %RANDOM
Rwork0.187 ---
obs0.187 57942 99.1 %-
Solvent computationSolvent model: FLAT MODEL / ksol: 0.75 e/Å3
Displacement parametersBiso mean: 20.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å20 Å2
2---0.98 Å20 Å2
3---0.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.04 Å
Refinement stepCycle: LAST / Resolution: 1.6→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2786 0 29 213 3028
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.771.5
X-RAY DIFFRACTIONc_mcangle_it2.492
X-RAY DIFFRACTIONc_scbond_it2.932
X-RAY DIFFRACTIONc_scangle_it4.232.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.252 497 5.2 %
Rwork0.206 8982 -
obs--98.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2TNP.PARTNP.TOP
X-RAY DIFFRACTION3PARAM19.IONTOPH19.ION
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.69
LS refinement shell
*PLUS
Rfactor Rfree: 0.252 / Rfactor Rwork: 0.206

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