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- PDB-4l2m: Crystal structure of the 2/2 hemoglobin from Synechococcus sp. PC... -

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Basic information

Entry
Database: PDB / ID: 4l2m
TitleCrystal structure of the 2/2 hemoglobin from Synechococcus sp. PCC 7002 in the cyanomet state and with covalently attached heme
ComponentsCyanoglobin
KeywordsUNKNOWN FUNCTION / group I 2/2 hemoglobin / GlbN / trHbN / cyanomet hemoglobin / histidine-heme covalent linkage / truncated hemoglobin
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Truncated hemoglobin, group 1 / Truncated hemoglobin / Bacterial-like globin / Globin/Protoglobin / Globins / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CYANIDE ION / HEME B/C / Group 1 truncated hemoglobin
Similarity search - Component
Biological speciesSynechococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsWenke, B.B. / Schlessman, J.L. / Heroux, A. / Lecomte, J.T.J.
CitationJournal: Proteins / Year: 2014
Title: The 2/2 hemoglobin from the cyanobacterium Synechococcus sp. PCC 7002 with covalently attached heme: Comparison of X-ray and NMR structures.
Authors: Wenke, B.B. / Lecomte, J.T. / Heroux, A. / Schlessman, J.L.
History
DepositionJun 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Experimental preparation
Revision 1.2Sep 18, 2013Group: Database references
Revision 1.3Feb 19, 2014Group: Database references
Revision 1.4Sep 20, 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 / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_type.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

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Assembly

Deposited unit
A: Cyanoglobin
B: Cyanoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0629
Polymers27,4852
Non-polymers1,5777
Water66737
1
A: Cyanoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4834
Polymers13,7421
Non-polymers7413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cyanoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5795
Polymers13,7421
Non-polymers8374
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.622, 40.951, 66.461
Angle α, β, γ (deg.)90.000, 111.210, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cyanoglobin


Mass: 13742.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. (bacteria) / Strain: PCC 7002 / Gene: glbN, SYNPCC7002_A1621 / Plasmid: pET3c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8RT58
#2: Chemical ChemComp-HEB / HEME B/C / HYBRID BETWEEN B AND C TYPE HEMES (PROTOPORPHYRIN IX CONTAINING FE)


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-CYN / CYANIDE ION / Cyanide


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1% v/v isopropanol, 2 M ammonium sulfate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2013
Details: Meridionally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 12396 / Num. obs: 12396 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 43.8 Å2 / Rmerge(I) obs: 0.108 / Χ2: 1.054 / Net I/σ(I): 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.25-2.315.10.4563.898651.181100
2.31-2.375.80.4628591.056100
2.37-2.445.70.4268881.081100
2.44-2.526.10.3548781.016100
2.52-2.616.10.2998881.151100
2.61-2.715.80.2468821.13899.9
2.71-2.836.20.1918741.06100
2.83-2.985.90.1538761.076100
2.98-3.176.40.1258861.02499.9
3.17-3.4260.0978971.01899.9
3.42-3.766.20.0828731.016100
3.76-4.36.10.0738850.93999.8
4.3-5.426.10.0719081.012100
5.42-505.90.0879371.02599.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S69

1s69


Resolution: 2.25→34.19 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.2914 / WRfactor Rwork: 0.2215 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7737 / SU B: 14.864 / SU ML: 0.228 / SU R Cruickshank DPI: 0.3919 / SU Rfree: 0.2782 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.392 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2881 609 5 %RANDOM
Rwork0.2179 ---
all0.2214 12279 --
obs0.2214 12279 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.81 Å2 / Biso mean: 46.3993 Å2 / Biso min: 20.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å21.32 Å2
2---1.16 Å2-0 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.25→34.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1934 0 105 37 2076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192080
X-RAY DIFFRACTIONr_bond_other_d0.0070.021944
X-RAY DIFFRACTIONr_angle_refined_deg1.72.0072832
X-RAY DIFFRACTIONr_angle_other_deg0.75434422
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6345244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.56824.717106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36815336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2021514
X-RAY DIFFRACTIONr_chiral_restr0.060.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022420
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02512
X-RAY DIFFRACTIONr_mcbond_it2.3362.941984
X-RAY DIFFRACTIONr_mcbond_other2.3372.94981
X-RAY DIFFRACTIONr_mcangle_it3.4594.3951224
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 47 -
Rwork0.246 846 -
all-893 -
obs-846 99.89 %
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)
10.62330.9706-0.30674.95561.54151.43780.1236-0.0515-0.1296-0.0308-0.1234-0.1942-0.1041-0.0739-0.00020.1642-0.0207-0.0130.12520.03820.2617-6.7125-4.29829.0018
22.50140.058-0.97835.41782.09781.7206-0.07340.2223-0.0359-0.0862-0.01180.1495-0.10450.06210.08520.0801-0.0010.01920.12260.00260.1461-4.13691.694222.5916
32.05640.56240.45261.01540.15810.61060.023-0.0382-0.22590.0979-0.0978-0.0628-0.05780.21920.07480.09210.00110.03090.1820.03150.16094.0328-0.539329.4167
41.3489-0.95070.33342.5835-0.18080.5606-0.0138-0.04930.0198-0.1360.07590.0132-0.0148-0.0955-0.06210.18710.01970.03250.1221-0.00710.085516.6832-12.58782.6704
519.9764-6.985921.0643.087-4.578934.289-0.0601-0.32830.56570.0130.0421-0.3296-0.0072-0.56250.0180.252-0.1655-0.03050.36860.0630.17734.366-16.99076.5874
61.67480.4335-0.46772.3412-1.77191.75-0.0804-0.1702-0.0752-0.09450.1677-0.0952-0.0813-0.3002-0.08740.15670.0190.05770.22390.04540.099116.7686-13.620313.5064
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 32
2X-RAY DIFFRACTION2A33 - 58
3X-RAY DIFFRACTION3A59 - 124
4X-RAY DIFFRACTION4B2 - 60
5X-RAY DIFFRACTION5B61 - 67
6X-RAY DIFFRACTION6B68 - 124

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