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- PDB-2nss: Nitrobenzene Modified Horse Heart Myoglobin -

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Basic information

Entry
Database: PDB / ID: 2nss
TitleNitrobenzene Modified Horse Heart Myoglobin
ComponentsMyoglobin
KeywordsOXYGEN STORAGE/TRANSPORT / nitroso / nitro / nitrite / nitric oxide / no / heme / myoglobin / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


oxygen transport / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / NITROSOBENZENE / Myoglobin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCopeland, D.M. / West, A.H. / Richter-Addo, G.B.
CitationJournal: To be Published
Title: Nitrosoalkane and Nitrosoarene Binding to Myoglobin and Heme Models
Authors: Copeland, D.M. / West, A.H. / Richter-Addo, G.B.
History
DepositionNov 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Aug 30, 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_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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3289
Polymers16,9841
Non-polymers1,3448
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.248, 28.847, 65.983
Angle α, β, γ (deg.)90.000, 105.630, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Myoglobin /


Mass: 16983.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / Organ: Heart / References: UniProt: P68082
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-NBE / NITROSOBENZENE / Nitrosobenzene


Mass: 107.110 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H5NO
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 1.78 Å3/Da / Density % sol: 35.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Ammonium sulfate, Tris-HCL, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 10, 2006 / Details: OSMIC MIRRORS
RadiationMonochromator: OSMIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→21.91 Å / Num. obs: 8578 / % possible obs: 97.5 % / Redundancy: 4.88 % / Rmerge(I) obs: 0.079 / Χ2: 0.97 / Net I/σ(I): 12.5 / Scaling rejects: 318
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2-2.074.60.3144.238728390.9693.6
2.07-2.154.810.2844.538587990.9497.7
2.15-2.254.930.2145.741948480.9795.8
2.25-2.374.840.1876.441148460.9896.9
2.37-2.524.930.1557.742718640.9498.1
2.52-2.715.010.1498.443078541.0297.2
2.71-2.9950.11310.743228580.9998.1
2.99-3.424.990.07217.143158580.9799
3.42-4.34.890.04626.143768790.9699
4.3-21.914.780.03931.54531933199.8

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Phasing

Phasing MRRfactor: 0.344 / Cor.coef. Fo:Fc: 0.734
Highest resolutionLowest resolution
Rotation3 Å27.13 Å
Translation3 Å27.13 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.2Ddata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NPG
Resolution: 2→19.74 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.918 / SU B: 5.354 / SU ML: 0.15 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.298 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.266 847 9.8 %RANDOM
Rwork0.181 ---
obs0.189 7789 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.01 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 93 90 1377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0211327
X-RAY DIFFRACTIONr_angle_refined_deg1.952.091788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9555151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84825.09453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.61915229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.822152
X-RAY DIFFRACTIONr_chiral_restr0.1270.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02983
X-RAY DIFFRACTIONr_nbd_refined0.2310.2649
X-RAY DIFFRACTIONr_nbtor_refined0.2990.2855
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.270
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.29
X-RAY DIFFRACTIONr_mcbond_it1.1341.5804
X-RAY DIFFRACTIONr_mcangle_it1.67821209
X-RAY DIFFRACTIONr_scbond_it2.9193617
X-RAY DIFFRACTIONr_scangle_it3.8374.5577
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.444 59 -
Rwork0.241 543 -
obs-602 92.9 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.63511.21824.41561.4122.9217.04520.1065-0.1445-0.18560.1001-0.05720.1571-0.0606-0.1102-0.0494-0.0761-0.0145-0.04450.01450.01270.0738-16.862-6.55316.705
26.0252-0.3049-2.90210.7340.8742.13360.2142-0.07780.02840.0321-0.1595-0.0781-0.0979-0.0144-0.0546-0.02140.0158-0.06990.04520.02950.01711.036-3.15122.599
319.39871.31372.72910.0890.18480.3839-0.0370.93750.11160.53150.15970.4657-0.84380.6067-0.1227-0.05570.0268-0.00820.11820.17660.156111.1811.31316.931
430.7734-7.32751.34037.7546-0.99220.13380.6959-1.3117-0.439-0.4738-0.3637-0.2785-0.63020.1363-0.3322-0.0218-0.0168-0.06510.10780.0059-0.08317.913-1.17330.517
54.84361.66183.18451.36671.812.7398-0.0407-0.02810.06150.01020.1250.0828-0.0303-0.1126-0.0844-0.0313-0.0082-0.03420.0281-0.0010.0398-6.2174.42321.671
612.39622.46971.35413.6374-0.23590.22920.1630.03650.50070.0632-0.10720.11410.0620.0077-0.0558-0.01440.0127-0.05090.063-0.0065-0.0247-5.7319.9137.285
72.27462.2533-2.68592.263-2.45934.4849-0.02750.0371-0.20480.0964-0.053-0.2025-0.1868-0.02940.0806-0.0559-0.0035-0.05750.0442-0.00570.0434-1.145-6.66115.571
81.52150.6084-0.88710.2435-0.35190.55510.10880.1269-0.01570.33190.04590.004-0.2105-0.038-0.1546-0.0435-0.0115-0.06890.0561-0.01620.0386-6.805-2.7495.708
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 20
2X-RAY DIFFRACTION2A21 - 36
3X-RAY DIFFRACTION3A37 - 41
4X-RAY DIFFRACTION4A51 - 57
5X-RAY DIFFRACTION5A58 - 77
6X-RAY DIFFRACTION6A82 - 96
7X-RAY DIFFRACTION7A100 - 119
8X-RAY DIFFRACTION8A124 - 150

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