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- PDB-3uhk: HBI (K96R) without ligand bound -

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Basic information

Entry
Database: PDB / ID: 3uhk
TitleHBI (K96R) without ligand bound
ComponentsGlobin-1
KeywordsOXYGEN STORAGE / OXYGEN TRANSPORT / allostery / oxygen binding
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / response to hypoxia / heme binding / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
: / Myoglobin-like, M family globin domain / 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 / Globin-1
Similarity search - Component
Biological speciesScapharca inaequivalvis (ark clam)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRen, Z. / Srajer, V. / Knapp, J.E. / Royer Jr., W.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Cooperative macromolecular device revealed by meta-analysis of static and time-resolved structures.
Authors: Ren, Z. / Srajer, V. / Knapp, J.E. / Royer, W.E.
History
DepositionNov 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 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 / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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

Downloads & links

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Assembly

Deposited unit
A: Globin-1
B: Globin-1
C: Globin-1
D: Globin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4478
Polymers63,9814
Non-polymers2,4664
Water4,252236
1
A: Globin-1
B: Globin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2244
Polymers31,9912
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-47 kcal/mol
Surface area12390 Å2
MethodPISA
2
C: Globin-1
D: Globin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2244
Polymers31,9912
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-48 kcal/mol
Surface area12590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.880, 44.040, 87.230
Angle α, β, γ (deg.)90.00, 115.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Globin-1 / Dimeric hemoglobin / Globin I / HbI


Mass: 15995.317 Da / Num. of mol.: 4 / Mutation: K96R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scapharca inaequivalvis (ark clam) / Plasmid: PCS-26 / Production host: Escherichia coli (E. coli) / Strain (production host): W3110LACIQ L8 / References: UniProt: P02213
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 296 K / Method: microbatch / pH: 7.5
Details: 2.1-2.3 M phosphate buffer, pH 7.5, MICROBATCH, temperature 296K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 23, 2000
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 39433 / Num. obs: 36200 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 10.4
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 3.8 / Rsym value: 0.278 / % possible all: 94.9

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SDH

3sdh


Resolution: 2→30.91 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1474448.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2913 8.1 %RANDOM
Rwork0.194 ---
all0.194 39433 --
obs0.194 36157 91.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.619 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 19.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å2-3.63 Å2
2--1.85 Å20 Å2
3----2.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2→30.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4472 0 172 236 4880
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.03
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.031.5
X-RAY DIFFRACTIONc_mcangle_it3.142
X-RAY DIFFRACTIONc_scbond_it5.382
X-RAY DIFFRACTIONc_scangle_it7.712.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.253 522 8.6 %
Rwork0.22 5527 -
obs--93.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2param19x.hemetoph19x.heme
X-RAY DIFFRACTION3water_rep.param

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