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- PDB-1drm: CRYSTAL STRUCTURE OF THE LIGAND FREE BJFIXL HEME DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1drm
TitleCRYSTAL STRUCTURE OF THE LIGAND FREE BJFIXL HEME DOMAIN
ComponentsSENSOR PROTEIN FIXL
KeywordsTRANSFERASE / FixL / heme domain / PAS family / two-component system / histidine kinase
Function / homology
Function and homology information


histidine phosphotransfer kinase activity / nitrogen fixation / histidine kinase / phosphorelay sensor kinase activity / regulation of DNA-templated transcription / ATP binding / metal ion binding
Similarity search - Function
PAS-associated, C-terminal / PAC domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / PAS domain / Signal transduction histidine kinase-related protein, C-terminal ...PAS-associated, C-terminal / PAC domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / PAS domain / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Beta-Lactamase / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Sensor protein FixL
Similarity search - Component
Biological speciesBradyrhizobium japonicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsGong, W. / Hao, B. / Mansy, S.S. / Gonzalez, G. / Gilles-Gonzalez, M.A. / Chan, M.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Structure of a biological oxygen sensor: a new mechanism for heme-driven signal transduction.
Authors: Gong, W. / Hao, B. / Mansy, S.S. / Gonzalez, G. / Gilles-Gonzalez, M.A. / Chan, M.K.
History
DepositionJan 6, 2000Deposition site: RCSB / Processing site: RCSB
SupersessionJan 24, 2000ID: 1BV6
Revision 1.0Jan 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SENSOR PROTEIN FIXL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5362
Polymers14,9201
Non-polymers6161
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.800, 128.800, 58.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein SENSOR PROTEIN FIXL /


Mass: 14919.858 Da / Num. of mol.: 1 / Fragment: HEME DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium japonicum (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P23222, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 3.15 Å3/Da / Density % sol: 60.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Sodium Chloride, MPD, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14.5 M1reservoirNaCl
25 %MPD1reservoir
30.1 MHEPES1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONNSLS X4A11.7396
SYNCHROTRONNSLS X4A21.7379
SYNCHROTRONNSLS X4A31.6984
SYNCHROTRONNSLS X4A41.4938
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.73961
21.73791
31.69841
41.49381
ReflectionResolution: 2.4→20 Å / Num. all: 31111 / Num. obs: 7104 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.076
Reflection shellResolution: 2.4→20 Å / Rmerge(I) obs: 0.221 / Num. unique all: 7104 / % possible all: 98
Reflection
*PLUS
Num. measured all: 31111
Reflection shell
*PLUS
% possible obs: 98 %

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.4→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 569 -RANDOM
Rwork0.199 ---
all0.199 31111 --
obs0.199 7104 97 %-
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms938 0 43 82 1063
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.675
X-RAY DIFFRACTIONx_bond_d0.014
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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