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- PDB-3lhb: THE 2.7 ANGSTROM CRYSTAL STRUCTURE OF DEOXYGENATED HEMOGLOBIN FRO... -

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Basic information

Entry
Database: PDB / ID: 3lhb
TitleTHE 2.7 ANGSTROM CRYSTAL STRUCTURE OF DEOXYGENATED HEMOGLOBIN FROM THE SEA LAMPREY (PETROMYZON MARINUS)
ComponentsPROTEIN (HEMOGLOBIN)
KeywordsMETAL BINDING PROTEIN / HEMOGLOBIN / OXYGEN TRANSPORT / BOHR EFFECT
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / oxidoreductase activity / iron ion binding / heme binding
Similarity search - Function
Globin, lamprey/hagfish type / 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-5
Similarity search - Component
Biological speciesPetromyzon marinus (sea lamprey)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHeaslet, H.A. / Royer Jr., W.E.
Citation
Journal: Structure Fold.Des. / Year: 1999
Title: The 2.7 A crystal structure of deoxygenated hemoglobin from the sea lamprey (Petromyzon marinus): structural basis for a lowered oxygen affinity and Bohr effect.
Authors: Heaslet, H.A. / Royer Jr., W.E.
#1: Journal: J.Mol.Biol. / Year: 1985
Title: Refinement of a Molcular Model for Lamprey Hemoglobin from Petromyzon Marinus
Authors: Honzatko, R.B. / Hendrickson, W.A. / Love, W.E.
#2: Journal: Nature New Biol. / Year: 1971
Title: Structure of Lamprey Hemoglobin
Authors: Hendrickson, W.A. / Love, W.E.
History
DepositionJan 12, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 20, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 6, 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_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_asym_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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (HEMOGLOBIN)
B: PROTEIN (HEMOGLOBIN)
C: PROTEIN (HEMOGLOBIN)
D: PROTEIN (HEMOGLOBIN)
E: PROTEIN (HEMOGLOBIN)
F: PROTEIN (HEMOGLOBIN)
G: PROTEIN (HEMOGLOBIN)
H: PROTEIN (HEMOGLOBIN)
I: PROTEIN (HEMOGLOBIN)
J: PROTEIN (HEMOGLOBIN)
K: PROTEIN (HEMOGLOBIN)
L: PROTEIN (HEMOGLOBIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,89824
Polymers195,50012
Non-polymers7,39812
Water00
1
A: PROTEIN (HEMOGLOBIN)
B: PROTEIN (HEMOGLOBIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8164
Polymers32,5832
Non-polymers1,2332
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: PROTEIN (HEMOGLOBIN)
D: PROTEIN (HEMOGLOBIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8164
Polymers32,5832
Non-polymers1,2332
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: PROTEIN (HEMOGLOBIN)
F: PROTEIN (HEMOGLOBIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8164
Polymers32,5832
Non-polymers1,2332
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: PROTEIN (HEMOGLOBIN)
H: PROTEIN (HEMOGLOBIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8164
Polymers32,5832
Non-polymers1,2332
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: PROTEIN (HEMOGLOBIN)
J: PROTEIN (HEMOGLOBIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8164
Polymers32,5832
Non-polymers1,2332
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: PROTEIN (HEMOGLOBIN)
L: PROTEIN (HEMOGLOBIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8164
Polymers32,5832
Non-polymers1,2332
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.630, 215.160, 75.390
Angle α, β, γ (deg.)90.00, 95.80, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.995624, 0.071172, 0.060553), (0.092939, 0.821627, 0.562398), (-0.009724, 0.565565, -0.824646)44.149, 32.9888, -112.2365
2given(0.952872, -0.196594, 0.231054), (-0.267964, -0.902493, 0.337198), (0.142233, -0.38322, -0.91264)20.2301, 395.7204, 114.4338
3given(-0.961494, 0.110635, -0.251572), (-0.063347, -0.97996, -0.188854), (-0.267425, -0.165646, 0.949234)58.0869, 424.65649, 10.8774
4given(0.927905, -0.366844, -0.066476), (-0.053753, 0.044804, -0.997549), (0.368923, 0.929203, 0.021855)55.0101, 272.76321, -176.1658
5given(-0.931105, 0.364485, -0.013948), (0.220629, 0.53234, -0.817274), (-0.290459, -0.764045, -0.576081)10.3483, 162.90961, 188.4144
6given(-0.995444, 0.013278, 0.094423), (0.095093, 0.211133, 0.972821), (-0.007018, 0.977367, -0.211434)52.2495, 151.72, -160.7388
7given(0.999983, 0.004353, 0.00377), (-0.005747, 0.712798, 0.701346), (0.000366, -0.701356, 0.712811)2.0204, 72.9975, 110.0027
8given(-0.945881, 0.034753, -0.322647), (0.278728, -0.422176, -0.8626), (-0.166192, -0.905847, 0.389642)39.6229, 271.63251, 132.2677
9given(0.962645, -0.081954, 0.258065), (0.072196, -0.840901, -0.536352), (0.260964, 0.534948, -0.803573)26.5062, 332.02689, -71.2118
10given(-0.922132, -0.317125, -0.221596), (0.043958, -0.654958, 0.754386), (-0.384371, 0.685902, 0.617898)84.1003, 270.78159, -111.4934
11given(0.921119, 0.276786, 0.273732), (-0.231941, -0.174512, 0.956948), (0.312639, -0.944952, -0.096548)-21.0991, 198.5798, 134.2494
DetailsTHE TWELVE PROTOMERS IN THE ASYMMETRIC UNIT FORM SIX ESSENTIALLY IDENTICAL DIMERS.

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Components

#1: Protein
PROTEIN (HEMOGLOBIN)


Mass: 16291.678 Da / Num. of mol.: 12 / Source method: isolated from a natural source
Details: COMPONENT FIVE(5) OF SIX(6) HEMOGLOBINS ISOLATED FROM P.MARINUS.
Source: (natural) Petromyzon marinus (sea lamprey) / Cell: RED BLOOD CELL / Cellular location: CYTOPLASM / References: UniProt: P02208
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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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: 2.46 Å3/Da / Density % sol: 47 %
Crystal growpH: 6.8 / Details: pH 6.8
Crystal
*PLUS
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
122 %PEG400011
2170 mMphosphate11

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Data collection

DiffractionMean temperature: 293.15 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 1, 1997
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→10 Å / Num. obs: 49184 / % possible obs: 94.7 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rsym value: 0.076 / Net I/σ(I): 12
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.422 / % possible all: 87.2
Reflection
*PLUS
Num. measured all: 147754 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 87.2 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2LHB

2lhb


Resolution: 2.7→10 Å / Isotropic thermal model: GROUP THERMAL FACTORS / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.232 5599 11.4 %RANDOM
Rwork0.195 ---
obs0.195 49184 94.7 %-
Displacement parametersBiso mean: 44.5 Å2
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13728 0 516 0 14244
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.364
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.261
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS / Rms dev position: 1.5 Å / Weight position: 300
LS refinement shellResolution: 2.7→2.8 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.329 449 10.9 %
Rwork0.287 3678 -
obs--87.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19X.HEMETOPH19X.HEME
X-RAY DIFFRACTION3PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 11.4 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 44.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.261
LS refinement shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / Rfactor Rfree: 0.329 / % reflection Rfree: 10.9 % / Rfactor Rwork: 0.287

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