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- PDB-3hix: Crystal Structure of the Rhodanese_3 like domain from Anabaena sp... -

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Basic information

Entry
Database: PDB / ID: 3hix
TitleCrystal Structure of the Rhodanese_3 like domain from Anabaena sp Alr3790 protein. Northeast Structural Genomics Consortium Target NsR437i
ComponentsAlr3790 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Alr3790 / rhodanese / rhodanese_3 / Q8YQN0 / Q8YQN0_ANASP / NSR437I / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


: / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAnabaena sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.92 Å
AuthorsVorobiev, S. / Chen, Y. / Forouhar, F. / Maglaqui, M. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. ...Vorobiev, S. / Chen, Y. / Forouhar, F. / Maglaqui, M. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the Rhodanese_3 like domain from Anabaena sp Alr3790 protein.
Authors: Vorobiev, S. / Chen, Y. / Forouhar, F. / Maglaqui, M. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionMay 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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_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: Alr3790 protein
B: Alr3790 protein
C: Alr3790 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1458
Polymers35,8703
Non-polymers2755
Water3,711206
1
A: Alr3790 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1224
Polymers11,9571
Non-polymers1653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alr3790 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0673
Polymers11,9571
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Alr3790 protein


Theoretical massNumber of molelcules
Total (without water)11,9571
Polymers11,9571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Alr3790 protein
hetero molecules

B: Alr3790 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1887
Polymers23,9132
Non-polymers2755
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area1830 Å2
ΔGint-36 kcal/mol
Surface area10060 Å2
MethodPISA
5
C: Alr3790 protein

C: Alr3790 protein


Theoretical massNumber of molelcules
Total (without water)23,9132
Polymers23,9132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area1260 Å2
ΔGint-14 kcal/mol
Surface area8480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.306, 105.479, 41.615
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Alr3790 protein


Mass: 11956.730 Da / Num. of mol.: 3 / Fragment: sequence database residues 24-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena sp. (bacteria) / Strain: PCC 7120 / Gene: alr3790 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q8YQN0
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.91 Å3/Da / Density % sol: 35.47 %
Crystal growTemperature: 277 K / pH: 6
Details: 20% PEG 4000, 0.1M manganese chloride, 0.1M MES, pH 6.0, Microbatch under paraffin oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9786
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.92→500 Å / Num. obs: 21563 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 14.2 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 37.6
Reflection shellHighest resolution: 1.92 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 3.9 / % possible all: 95.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXDEphasing
RESOLVEmodel building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.92→34.61 Å / SU ML: 0.43 / σ(F): 1.91 / Stereochemistry target values: ML
Details: TLS DETAILS. NUMBER OF TLS GROUPS: 3 ORIGIN: CENTER OF MASS TLS GROUP : 1 SELECTION: chain A ORIGIN FOR THE GROUP (A): 21.6286 35.3809 -3.2102 T TENSOR T11: 0.0624 T22: 0.1527 T33: 0.1155 ...Details: TLS DETAILS. NUMBER OF TLS GROUPS: 3 ORIGIN: CENTER OF MASS TLS GROUP : 1 SELECTION: chain A ORIGIN FOR THE GROUP (A): 21.6286 35.3809 -3.2102 T TENSOR T11: 0.0624 T22: 0.1527 T33: 0.1155 T12: 0.0177 T13: 0.0028 T23: 0.0021 L TENSOR L11: 1.3258 L22: 0.9000 L33: 1.2612 L12: -0.1670 L13: 1.0507 L23: -0.3704 S TENSOR S11: -0.1360 S12: 0.0069 S13: 0.0464 S21: 0.0477 S22: 0.0383 S23: 0.0000 S31: -0.2015 S32: -0.0132 S33: -0.2878 TLS GROUP : 2 SELECTION: chain B ORIGIN FOR THE GROUP (A): 42.5423 32.7700 24.7352 T TENSOR T11: 0.3628 T22: 0.1203 T33: 0.1251 T12: -0.0085 T13: -0.0376 T23: 0.0201 L TENSOR L11: 1.4097 L22: 0.3349 L33: 0.8316 L12: 0.6542 L13: -0.3603 L23: -0.3371 S TENSOR S11: 0.1203 S12: 0.0108 S13: 0.0659 S21: 0.3051 S22: -0.1410 S23: 0.0289 S31: -0.5626 S32: -0.0803 S33: -0.1710 TLS GROUP : 3 SELECTION: chain C ORIGIN FOR THE GROUP (A): 50.2033 53.9437 13.5016 T TENSOR T11: 0.1434 T22: 0.1161 T33: 0.1814 T12: 0.0063 T13: -0.0092 T23: -0.0202 L TENSOR L11: 0.6296 L22: 0.8678 L33: 0.3256 L12: -0.1594 L13: 0.2343 L23: -0.2656 S TENSOR S11: -0.0424 S12: 0.1661 S13: -0.0522 S21: -0.2500 S22: 0.0465 S23: -0.0200 S31: 0.1290 S32: 0.0377 S33: -0.0000
RfactorNum. reflection% reflection
Rfree0.23 2045 5.08 %
Rwork0.214 --
obs0.215 21517 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.73 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.1846 Å2-0 Å2-0 Å2
2---0.4771 Å2-0 Å2
3----6.7075 Å2
Refinement stepCycle: LAST / Resolution: 1.92→34.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2098 0 5 206 2309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062139
X-RAY DIFFRACTIONf_angle_d1.3322890
X-RAY DIFFRACTIONf_dihedral_angle_d17.211758
X-RAY DIFFRACTIONf_chiral_restr0.09313
X-RAY DIFFRACTIONf_plane_restr0.006383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.96410.2531440.24982309X-RAY DIFFRACTION91
1.9641-2.01330.27631810.25992492X-RAY DIFFRACTION99
2.0133-2.06770.28791180.25952599X-RAY DIFFRACTION100
2.0677-2.12850.28941020.24322577X-RAY DIFFRACTION100
2.1285-2.19720.25171450.24382567X-RAY DIFFRACTION100
2.1972-2.27570.27321570.21982536X-RAY DIFFRACTION100
2.2757-2.36680.23611450.23062543X-RAY DIFFRACTION100
2.3668-2.47450.22481610.20542546X-RAY DIFFRACTION100
2.4745-2.60490.25251210.22112591X-RAY DIFFRACTION100
2.6049-2.76810.23651400.222555X-RAY DIFFRACTION100
2.7681-2.98170.2391460.23382578X-RAY DIFFRACTION100
2.9817-3.28150.20021400.21282520X-RAY DIFFRACTION100
3.2815-3.75590.19691080.19052601X-RAY DIFFRACTION100
3.7559-4.73010.17851190.17062582X-RAY DIFFRACTION100
4.7301-34.61150.23041180.20032583X-RAY DIFFRACTION100
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)
11.3258-0.1671.05070.9-0.37041.2612-0.1360.00690.04640.04770.03830-0.2015-0.0132-0.28780.06240.01770.00280.15270.00210.115521.628635.3809-3.2102
21.40970.6542-0.36030.3349-0.33710.83160.12030.01080.06590.3051-0.1410.0289-0.5626-0.0803-0.1710.3628-0.0085-0.03760.12030.02010.125142.542332.7724.7352
30.6296-0.15940.23430.8678-0.26560.3256-0.04240.1661-0.0522-0.250.0465-0.020.1290.0377-00.14340.0063-0.00920.1161-0.02020.181450.203353.943713.5016
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

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