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- PDB-3zhw: X-ray Crystallographic Structural Characteristics of Arabidopsis ... -

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Basic information

Entry
Database: PDB / ID: 3zhw
TitleX-ray Crystallographic Structural Characteristics of Arabidopsis Hemoglobin I and their Functional Implications
ComponentsNON-SYMBIOTIC HEMOGLOBIN 1
KeywordsOXYGEN BINDING
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors; With a cytochrome as acceptor / plant-type cell wall / plasmodesma / oxygen binding / cellular response to hypoxia / response to hypoxia / oxidoreductase activity / heme binding / metal ion binding / nucleus ...Oxidoreductases; Acting on other nitrogenous compounds as donors; With a cytochrome as acceptor / plant-type cell wall / plasmodesma / oxygen binding / cellular response to hypoxia / response to hypoxia / oxidoreductase activity / heme binding / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Leghaemoglobin, iron-binding site / Plant hemoglobins signature. / Leghaemoglobin / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Leghaemoglobin, iron-binding site / Plant hemoglobins signature. / Leghaemoglobin / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Anaerobic nitrite reductase AHB1
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsMukhi, N. / Dhindwal, S. / Uppal, S. / Kumar, P. / Kaur, J. / Kundu, S.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: X-Ray Crystallographic Structural Characteristics of Arabidopsis Hemoglobin I and Their Functional Implications
Authors: Mukhi, N. / Dhindwal, S. / Uppal, S. / Kumar, P. / Kaur, J. / Kundu, S.
History
DepositionDec 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2Aug 7, 2013Group: Database references
Revision 1.3Feb 12, 2014Group: Source and taxonomy
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_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: NON-SYMBIOTIC HEMOGLOBIN 1
B: NON-SYMBIOTIC HEMOGLOBIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7378
Polymers36,1202
Non-polymers1,6176
Water2,468137
1
A: NON-SYMBIOTIC HEMOGLOBIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9655
Polymers18,0601
Non-polymers9054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NON-SYMBIOTIC HEMOGLOBIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7733
Polymers18,0601
Non-polymers7132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.280, 76.672, 98.228
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NON-SYMBIOTIC HEMOGLOBIN 1 / ARATH GLB1 / HB1


Mass: 18060.135 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O24520
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 3.1 Å3/Da / Density % sol: 60.35 % / Description: NONE
Crystal growpH: 7
Details: AMMONIUM SULFATE, CACODYLATE TRIHYDRATE, PEG 8000 AND GLYCEROL, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 21, 2011 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. obs: 22216 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.16
Reflection shellResolution: 2.21→2.25 Å / Redundancy: 3 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2 / % possible all: 56

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QQQ

3qqq


Resolution: 2.22→46.94 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 12.874 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2623 1129 5.1 %RANDOM
Rwork0.21435 ---
obs0.21669 21035 97.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.763 Å2
Baniso -1Baniso -2Baniso -3
1-2.31 Å20 Å20 Å2
2---0.71 Å20 Å2
3----1.6 Å2
Refinement stepCycle: LAST / Resolution: 2.22→46.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2427 0 106 137 2670
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192587
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1282.0133503
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7155305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.724.62493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.49915477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.183158
X-RAY DIFFRACTIONr_chiral_restr0.0810.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211862
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_it1.1563.0461226
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9284.5631529
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.563.2771361
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 2.221→2.279 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 67 -
Rwork0.383 1197 -
obs--76.37 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1321-0.5558-0.37491.18830.35381.47070.0920.03710.0396-0.08640.00580.0396-0.1111-0.0861-0.09790.0939-0.00640.0180.04530.02640.0331-27.80475.65282.0864
21.04680.51410.4111.68870.16771.60750.06850.0228-0.04650.1401-0.0349-0.08410.03230.0898-0.03360.0559-0.0093-0.00810.04140.01240.0139-26.9646-19.426516.3581
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B8 - 160
2X-RAY DIFFRACTION2A6 - 159

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