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- PDB-1bhy: LOW TEMPERATURE MIDDLE RESOLUTION STRUCTURE OF P64K FROM MASC DATA -

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Basic information

Entry
Database: PDB / ID: 1bhy
TitleLOW TEMPERATURE MIDDLE RESOLUTION STRUCTURE OF P64K FROM MASC DATA
ComponentsP64K
KeywordsOUTER MEMBRANE PROTEIN / MASC / MULTIWAVELENGTH ANOMALOUS SOLVENT CONTRAST
Function / homology
Function and homology information


dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase (NADH) activity / 2-oxoglutarate metabolic process / flavin adenine dinucleotide binding
Similarity search - Function
Dihydrolipoamide dehydrogenase / : / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Biotin-requiring enzyme ...Dihydrolipoamide dehydrogenase / : / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Dihydrolipoyl dehydrogenase
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, RIGID BODY REFINEMENT / Resolution: 4.18 Å
AuthorsRamin, M. / Shepard, W. / Fourme, R. / Kahn, R.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Multiwavelength anomalous solvent contrast (MASC): derivation of envelope structure-factor amplitudes and comparison with model values.
Authors: Ramin, M. / Shepard, W. / Fourme, R. / Kahn, R.
#1: Journal: J.Mol.Biol. / Year: 1997
Title: Molecular Structure of the Lipoamide Dehydrogenase Domain of a Surface Antigen from Neisseria Meningitidis
Authors: Li De La Sierra, I. / Pernot, L. / Prange, T. / Saludjian, P. / Schiltz, M. / Fourme, R. / Padron, G.
History
DepositionJun 10, 1998Processing site: BNL
Revision 1.0Nov 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.type / _software.name
Revision 1.4Aug 2, 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_leaving_atom_flag / _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 1.5Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_PDB_caveat / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P64K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5842
Polymers50,7981
Non-polymers7861
Water00
1
A: P64K
hetero molecules

A: P64K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,1674
Polymers101,5962
Non-polymers1,5712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area11110 Å2
ΔGint-67 kcal/mol
Surface area35180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)140.620, 140.620, 77.020
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 P64K


Mass: 50797.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neisseria meningitidis (bacteria) / References: UniProt: Q51225
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
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: 3.6 Å3/Da / Density % sol: 60.5 %
Crystal growDetails: PROTEIN WAS CRYSTALLIZED FROM AMMONIUM SULPHATE
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion, hanging drop
Details: Li De La Sierra, I., (1994) J.Mol.Biol., 235, 1154.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-20 mg/mlprotein1drop
20.02 MTris-HCl1drop
30.006 MEDTA1drop
40.15 M1dropNaCl
50.1 Mpotassium phosphate1reservoir
62 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 124 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 0.99
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1995 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 4.18→100 Å / Num. obs: 6008 / % possible obs: 98.2 % / Observed criterion σ(I): 3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 5.2
Reflection shellResolution: 4.18→4.29 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 10.7 / Rsym value: 0.06 / % possible all: 78
Reflection
*PLUS
Num. measured all: 44222

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
Agrovata(CCP4)data reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4(AGROVATAdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, RIGID BODY REFINEMENT
Starting model: 1OJT

1ojt


Resolution: 4.18→8 Å / Cross valid method: THROUGHOUT
Rfactor% reflectionSelection details
Rfree0.323 10 %RANDOM
Rwork0.338 --
obs0.338 --
Refinement stepCycle: LAST / Resolution: 4.18→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3563 0 53 0 3616

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