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- PDB-4xpw: Crystal structures of Leu114F mutant -

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Basic information

Entry
Database: PDB / ID: 4xpw
TitleCrystal structures of Leu114F mutant
ComponentsBacteriohemerythrin
KeywordsOXYGEN BINDING PROTEIN
Function / homology
Function and homology information


oxygen carrier activity / metal ion binding
Similarity search - Function
Hemerythrin-like / Hemerythrin, metal-binding domain / Haemerythrin, iron-binding site / Hemerythrin-like superfamily / : / Hemerythrin family signature. / Hemerythrin-like / Hemerythrin HHE cation binding domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Bacteriohemerythrin
Similarity search - Component
Biological speciesMethylococcus capsulatus str. Bath (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å
AuthorsChuankhayan, P. / Chen, K.H.C. / Wu, H.H. / Chen, C.J. / Fukuda, M. / Yu, S.S.F. / Chan, S.I.
CitationJournal: J.Inorg.Biochem. / Year: 2015
Title: The bacteriohemerythrin from Methylococcus capsulatus (Bath): Crystal structures reveal that Leu114 regulates a water tunnel.
Authors: Chen, K.H.C. / Chuankhayan, P. / Wu, H.H. / Chen, C.J. / Fukuda, M. / Yu, S.S.F. / Chan, S.I.
History
DepositionJan 18, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Dec 9, 2015Group: Database references
Revision 1.3Jul 18, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_nat / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _citation.journal_id_CSD / _entity.pdbx_mutation ..._citation.journal_id_CSD / _entity.pdbx_mutation / _entity_src_nat.pdbx_organism_scientific / _entity_src_nat.strain / _pdbx_struct_oper_list.symmetry_operation / _struct_ref_seq_dif.details
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriohemerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9744
Polymers14,7711
Non-polymers2043
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint-18 kcal/mol
Surface area6970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.281, 83.281, 30.959
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein Bacteriohemerythrin / McHr


Mass: 14770.685 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Methylococcus capsulatus str. Bath (bacteria)
Strain: Bath / References: UniProt: Q60AX2
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: PEG 400, ammonium acetate, HEPES / PH range: 7-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.17→24.84 Å / Num. obs: 39403 / % possible obs: 99.4 % / Redundancy: 4.2 % / Rsym value: 0.065 / Net I/σ(I): 2.6
Reflection shellResolution: 1.17→1.21 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.61 / Num. unique all: 39403 / Rsym value: 0.426 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XPX

4xpx


Resolution: 1.17→24.84 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.409 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.16459 2085 5 %RANDOM
Rwork0.15193 ---
obs0.15256 39403 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.385 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.17→24.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1036 0 10 147 1193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0191064
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2861.9191433
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4265130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49225.09453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.77115183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.281153
X-RAY DIFFRACTIONr_chiral_restr0.3950.2155
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02805
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9780.85523
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4031.276652
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0381.06541
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.0278.8081847
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.17→1.2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 153 -
Rwork0.219 2690 -
obs--93.03 %

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