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- PDB-5d1v: Crystal Structure and Thermal Stability of Hemoglobin from Thermo... -

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Basic information

Entry
Database: PDB / ID: 5d1v
TitleCrystal Structure and Thermal Stability of Hemoglobin from Thermophilic Phototrophic Bacterium Chloroflexus aurantiacus
ComponentsGlobin
KeywordsOXYGEN TRANSPORT / truncated Hemoglobin / temperature stability
Function / homology
Function and homology information


thioredoxin peroxidase activity / oxygen transport / cell redox homeostasis / oxygen binding / cellular response to oxidative stress / heme binding / metal ion binding / cytoplasm
Similarity search - Function
Globin, bacterial-like, conserved site / Protozoan/cyanobacterial globins signature. / Truncated hemoglobin / Bacterial-like globin / Globin/Protoglobin / Globins / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Globin
Similarity search - Component
Biological speciesChloroflexus aurantiacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsFromme, R. / Holl, M. / Tang, J.K.
CitationJournal: To Be Published
Title: Crystal Structure and Thermal Stability of Hemoglobin from Thermophilic Phototrophic Bacterium Chloroflexus aurantiacus
Authors: Fromme, R. / Holl, M. / Tang, J.K.
History
DepositionAug 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Globin
B: Globin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9774
Polymers29,7442
Non-polymers1,2332
Water8,341463
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-45 kcal/mol
Surface area12610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.960, 41.298, 72.117
Angle α, β, γ (deg.)90.00, 107.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Globin /


Mass: 14871.950 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 201 is Hemoglobin
Source: (gene. exp.) Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl) (bacteria)
Strain: ATCC 29366 / DSM 635 / J-10-fl / Gene: Caur_0123 / Plasmid: glbO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9WBH0
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C34H32FeN4O4 / Details: 201 is Hemoglobin
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 45.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 200 mM ammonium fluoride 20-30 mM HEPES pH 7.0 16-20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.74→19.59 Å / Num. obs: 27141 / % possible obs: 99 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 26.6
Reflection shellResolution: 1.74→1.802 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 6.49 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIXdev_1938refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→19.59 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0.25 / Phase error: 19.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1872 1339 4.93 %
Rwork0.1495 --
obs0.1514 27141 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.74→19.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2090 0 0 463 2553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112164
X-RAY DIFFRACTIONf_angle_d1.3082950
X-RAY DIFFRACTIONf_dihedral_angle_d14.914820
X-RAY DIFFRACTIONf_chiral_restr0.051268
X-RAY DIFFRACTIONf_plane_restr0.008392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.77160.26771040.20052637X-RAY DIFFRACTION99
1.7716-1.80570.22821350.20642656X-RAY DIFFRACTION100
1.8057-1.84250.25321440.19372601X-RAY DIFFRACTION100
1.8425-1.88250.23511560.19232651X-RAY DIFFRACTION100
1.8825-1.92630.23311150.18162615X-RAY DIFFRACTION100
1.9263-1.97440.22911110.17192709X-RAY DIFFRACTION100
1.9744-2.02780.20081430.16112645X-RAY DIFFRACTION100
2.0278-2.08740.18091520.15792597X-RAY DIFFRACTION100
2.0874-2.15470.18631410.1512679X-RAY DIFFRACTION100
2.1547-2.23160.19831480.15592630X-RAY DIFFRACTION100
2.2316-2.32080.22391160.15272669X-RAY DIFFRACTION99
2.3208-2.42620.2151390.14652614X-RAY DIFFRACTION100
2.4262-2.55390.22161190.14732622X-RAY DIFFRACTION99
2.5539-2.71350.19831210.14322700X-RAY DIFFRACTION100
2.7135-2.92240.19291660.14662586X-RAY DIFFRACTION99
2.9224-3.21530.15491760.14012577X-RAY DIFFRACTION100
3.2153-3.6780.15661330.12652665X-RAY DIFFRACTION99
3.678-4.62390.16411560.12222594X-RAY DIFFRACTION99
4.6239-19.66950.14571190.14962620X-RAY DIFFRACTION99
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)
11.55750.2874-0.24082.5375-0.6541.9307-0.06-0.07130.02440.17840.0399-0.2508-0.1170.1091-0.01880.07590.0107-0.0370.1093-0.01580.098826.37144.308243.6497
23.0393-1.49361.63864.3389-3.07955.09070.00190.1015-0.08480.140.0649-0.2856-0.10960.17820.02470.0565-0.01510.00540.1106-0.02310.148929.76011.934737.0069
32.1419-0.5431-1.40933.1971.18921.4343-0.09010.11510.0327-0.08180.0907-0.4785-0.02250.30650.10070.0621-0.01370.03110.17160.02990.151231.44652.430729.7507
45.50894.423-3.85714.534-3.56474.6649-0.14530.318-0.3616-0.22420.0710.00040.29110.05530.33480.1397-0.00590.03230.1504-0.01960.1222.6777-5.914229.9924
52.34380.66260.35113.4560.46052.833-0.0525-0.1280.03740.1846-0.0510.0933-0.1336-0.15340.08910.08240.02860.00510.10380.01260.04916.5657-0.504244.8514
65.2031.74252.6350.84022.05746.7381-0.1882-0.06270.48950.4396-0.0162-0.2535-0.79030.04010.560.2439-0.0249-0.06980.1035-0.03180.20220.803918.160141.2259
72.59561.34470.05445.41280.33181.9667-0.0428-0.08420.01510.23610.10970.1278-0.0403-0.1028-0.00530.05790.02210.00460.08810.00390.058514.1153.547437.7119
81.9806-0.3951.01631.9465-1.12640.98150.2398-0.34210.3980.4249-0.06050.2416-0.4429-0.37340.32750.40710.12150.04710.2052-0.19420.2637-9.889329.400161.0016
92.6313-1.9801-0.49914.79940.8042.02550.09470.03890.0711-0.3643-0.14620.0241-0.1264-0.13550.06190.1780.04850.01180.13970.00020.07580.048115.20150.1241
101.2842-0.2984-0.17012.11010.67481.461-0.0568-0.015-0.1073-0.1827-0.18880.4475-0.1062-0.32650.05070.14170.0471-0.02190.1799-0.04490.1589-9.416111.507455.067
112.7924-2.75710.53253.6932-1.10030.8926-0.1578-0.5709-0.4120.6875-0.2640.95880.4284-0.3838-0.08840.24780.01750.10680.2648-0.02120.3058-9.41045.451965.2911
120.8404-0.4126-0.322.92350.71911.89250.0183-0.02940.0414-0.0865-0.0111-0.3524-0.09330.12210.03610.12430.03260.00470.13930.00750.09164.469313.663858.2313
131.6748-1.14150.10377.7176-0.09592.2352-0.011-0.02060.00070.11070.003-0.1453-0.05260.1060.07330.1489-0.00530.00240.1291-0.00140.07342.657414.934965.0896
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 41 )
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 55 )
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 66 )
4X-RAY DIFFRACTION4chain 'A' and (resid 67 through 74 )
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 98 )
6X-RAY DIFFRACTION6chain 'A' and (resid 99 through 104 )
7X-RAY DIFFRACTION7chain 'A' and (resid 105 through 123 )
8X-RAY DIFFRACTION8chain 'B' and (resid 3 through 11 )
9X-RAY DIFFRACTION9chain 'B' and (resid 12 through 33 )
10X-RAY DIFFRACTION10chain 'B' and (resid 34 through 66 )
11X-RAY DIFFRACTION11chain 'B' and (resid 67 through 74 )
12X-RAY DIFFRACTION12chain 'B' and (resid 75 through 104 )
13X-RAY DIFFRACTION13chain 'B' and (resid 105 through 123 )

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