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- PDB-4max: Crystal structure of Synechococcus sp. PCC 7002 globin at cryogen... -

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Basic information

Entry
Database: PDB / ID: 4max
TitleCrystal structure of Synechococcus sp. PCC 7002 globin at cryogenic temperature with heme modification
Componentscyanoglobin
KeywordsUNKNOWN FUNCTION / hemeprotein / 2/2 hemoglobin / glbN / trhbN / 2/2 globin / ROS/RNS detoxification
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
HEME B/C / Group 1 truncated hemoglobin
Similarity search - Component
Biological speciesSynechococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.444 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
DepositionAug 18, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionAug 28, 2013ID: 4I0V
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Database references
Revision 1.2Feb 19, 2014Group: Database references
Revision 1.3Sep 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_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

Downloads & links

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Assembly

Deposited unit
A: cyanoglobin
B: cyanoglobin
C: cyanoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,85114
Polymers41,2273
Non-polymers2,62411
Water4,774265
1
A: cyanoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5534
Polymers13,7421
Non-polymers8113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cyanoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6495
Polymers13,7421
Non-polymers9074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: cyanoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6495
Polymers13,7421
Non-polymers9074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.791, 68.791, 156.059
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein cyanoglobin


Mass: 13742.418 Da / Num. of mol.: 3
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.: 3 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.24 Å3/Da / Density % sol: 45.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 7% glycerol, 2 M ammonium sulfate, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2012
Details: Meridionally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.444→50 Å / Num. all: 67233 / Num. obs: 67233 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.2 % / Rmerge(I) obs: 0.087 / Χ2: 2.244 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.444-1.485.90.3824.54431981.02895.5
1.48-1.570.36432911.12198.4
1.5-1.538.60.33232811.18499.1
1.53-1.5610.90.30333281.30599.7
1.56-1.612.30.2833401.279100
1.6-1.6313.40.25533671.345100
1.63-1.6715.20.22933281.472100
1.67-1.72150.20333731.458100
1.72-1.7715.10.17833661.527100
1.77-1.8315.40.15533481.678100
1.83-1.8914.70.13733521.732100
1.89-1.9715.50.13634121.99100
1.97-2.0614.90.10533662.226100
2.06-2.1715.60.09533972.44100
2.17-2.311.70.0933032.68597.1
2.3-2.4815.40.0834172.896100
2.48-2.7315.20.07534353.157100
2.73-3.1214.70.07234753.604100
3.12-3.9413.70.07131094.17788.7
3.94-5012.30.07437474.65499.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å41.49 Å
Translation2.5 Å41.49 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RTX

1rtx


Resolution: 1.444→41.49 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.1958 / WRfactor Rwork: 0.1772 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8994 / SU B: 1.569 / SU ML: 0.039 / SU R Cruickshank DPI: 0.0681 / SU Rfree: 0.0672 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1937 3410 5.1 %RANDOM
Rwork0.1732 ---
all0.1742 67144 --
obs0.1742 67144 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.15 Å2 / Biso mean: 17.0445 Å2 / Biso min: 6.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0 Å2-0 Å2
2---0.03 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.444→41.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2901 0 169 265 3335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193356
X-RAY DIFFRACTIONr_bond_other_d00.023194
X-RAY DIFFRACTIONr_angle_refined_deg1.7172.0134609
X-RAY DIFFRACTIONr_angle_other_deg0.66137322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1215431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.51824.743175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7715588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9281525
X-RAY DIFFRACTIONr_chiral_restr0.0720.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.023941
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02829
X-RAY DIFFRACTIONr_mcbond_it1.010.891539
X-RAY DIFFRACTIONr_mcbond_other1.0030.8891538
X-RAY DIFFRACTIONr_mcangle_it1.4151.331935
LS refinement shellResolution: 1.444→1.482 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 219 -
Rwork0.205 4407 -
all-4626 -
obs-4407 93.8 %
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)
10.4828-0.0476-0.04580.59430.20790.8947-0.0059-0.0351-0.01260.00760.0205-0.02940.03260.0086-0.01460.0413-0.00110.00260.05010.00590.044925.9492.41-2.437
22.12535.0760.419812.17790.70262.5098-0.10960.0125-0.4027-0.2811-0.0094-0.98810.19650.29010.1190.03060.02270.05210.03540.0150.149338.778-3.043-10.669
32.4045-1.1373-2.29871.693.09975.73370.013-0.160.1727-0.07670.1588-0.1037-0.13580.322-0.17180.0317-0.02230.01370.05910.00860.076432.31214.172-2.235
40.6726-0.50510.02981.03060.11970.5562-0.00280.0027-0.04670.0255-0.00620.06890.0232-0.04830.00910.0514-0.0048-0.00770.0430.00030.02757.7869.112-19.737
58.41540.4770.78491.7435-1.09162.0308-0.00260.2497-0.1948-0.26020.0180.0875-0.0013-0.1853-0.01530.07080.0233-0.01950.0984-0.00750.021912.656.284-34.148
63.7473-0.12083.92164.85542.31255.33170.0459-0.1286-0.1258-0.0549-0.03270.24050.026-0.1609-0.01320.0193-0.02-0.00160.0738-0.01840.0503-5.410.852-25.019
71.1129-0.1885-0.49780.79290.22281.1196-0.0224-0.0351-0.04620.0629-0.00160.0820.0294-0.03590.02390.0583-0.0088-0.00580.02210.00280.07236.012-11.777-5.725
82.7496-0.7329-0.83712.83480.35754.6741-0.02950.3469-0.5053-0.0812-0.16190.19250.21170.01150.19140.0703-0.01220.0010.0538-0.06490.10977.085-23.183-14.329
92.8967-0.9631-0.79377.8496-0.25535.0305-0.07380.0214-0.26590.12570.07210.39240.4655-0.11170.00160.0953-0.00510.0170.00780.01710.08386.289-20.9283.615
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 96
2X-RAY DIFFRACTION2A97 - 110
3X-RAY DIFFRACTION3A111 - 124
4X-RAY DIFFRACTION4B2 - 94
5X-RAY DIFFRACTION5B95 - 113
6X-RAY DIFFRACTION6B114 - 124
7X-RAY DIFFRACTION7C2 - 86
8X-RAY DIFFRACTION8C87 - 111
9X-RAY DIFFRACTION9C112 - 124

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