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- PDB-3o14: Crystal structure of an anti-ECFsigma factor, ChrR (Maqu_0586) fr... -

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Basic information

Entry
Database: PDB / ID: 3o14
TitleCrystal structure of an anti-ECFsigma factor, ChrR (Maqu_0586) from MARINOBACTER AQUAEOLEI VT8 at 1.70 A resolution
ComponentsAnti-ECFsigma factor, ChrR
KeywordsGENE REGULATION / CHRR / CUPIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


ChrR-like cupin domain / ChrR Cupin-like domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICOTINIC ACID / Anti-ECFsigma factor, ChrR
Similarity search - Component
Biological speciesMarinobacter aquaeolei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of an anti-ECFsigma factor, ChrR (Maqu_0586) from Marinobacter aquaeolei VT8 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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.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: Anti-ECFsigma factor, ChrR
B: Anti-ECFsigma factor, ChrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,01526
Polymers49,2872
Non-polymers1,72724
Water10,016556
1
A: Anti-ECFsigma factor, ChrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,58314
Polymers24,6441
Non-polymers93913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Anti-ECFsigma factor, ChrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,43212
Polymers24,6441
Non-polymers78811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.105, 45.773, 65.892
Angle α, β, γ (deg.)75.960, 71.080, 63.350
Int Tables number1
Space group name H-MP1
DetailsCRYSTAL PACKING ANALYSIS AND SIZE-EXCLUSION CHROMATOGRAPHY IN COMBINATION WITH STATIC LIGHT SCATTERING SUPPORT THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Anti-ECFsigma factor, ChrR


Mass: 24643.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinobacter aquaeolei (bacteria) / Strain: ATCC 700491 / DSM 11845 / VT8 / Gene: Maqu_0586 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A1TY68

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Non-polymers , 5 types, 580 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NIO / NICOTINIC ACID


Mass: 123.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.27 Å3/Da / Density % sol: 45.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 10.9
Details: 0.2000M lithium sulfate, 2.5000M ammonium sulfate, 0.1M CAPS pH 10.9, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97936
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 13, 2010 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979361
ReflectionResolution: 1.7→29.402 Å / Num. all: 46352 / Num. obs: 46352 / % possible obs: 97.3 % / Redundancy: 2 % / Biso Wilson estimate: 11.168 Å2 / Rsym value: 0.074 / Net I/σ(I): 7.4
Reflection shell

Diffraction-ID: 1 / Redundancy: 2 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.740.3172.4675133940.31795.8
1.74-1.790.2572.9645932570.25796.2
1.79-1.840.222.3640632310.2296.4
1.84-1.90.1824.1630931750.18296.5
1.9-1.960.1544.6598330090.15496.6
1.96-2.030.1255.9581529210.12597
2.03-2.110.1056.6574228810.10597.1
2.11-2.190.0976.2545827400.09797.1
2.19-2.290.0858.1524126340.08597.6
2.29-2.40.0778.6503625270.07797.7
2.4-2.530.0778.5483524300.07797.9
2.53-2.690.0718.9449822580.07198
2.69-2.870.0610.3428021460.0698.1
2.87-3.10.05112.2398920030.05198.6
3.1-3.40.04313.1369818570.04398.5
3.4-3.80.051.3333916780.0599
3.8-4.390.03713.1295614820.03798.9
4.39-5.380.0379.6246612370.03799
5.38-7.60.04212.419599810.04299.4
7.6-29.4020.0469.410205110.04697.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMAC5.5.0110refinement
SCALA3.3.15data scaling
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→29.402 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0.19 / SU B: 3.614 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.101
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 6. X-RAY FLUORESCENCE EXCITATION AND WAVELENGTH SCANS AND ANOMALOUS DIFFERENCE FOURIERS SUPPORT THE MODELING OF ZINC (ZN) IONS. GEOMETRIC RESTRAINTS WERE INCLUDED BETWEEN THE ZINC IONS AND THE COORDINATING ATOMS FROM THE GLUTAMATE AND HISTIDINE SIDE CHAINS. 7. SULFATE (SO4) AND 1,2-ETHANEDIOL (EDO) FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED. 8. NICOTINIC ACID (NIO) IS MODELED BASED ON THE SHAPE OF THE DENSITY AND HYDROGEN BOND DONOR/ACCEPTOR LOCATIONS. IT COULD BE SOME OTHER SIMILAR COMPOUND.
RfactorNum. reflection% reflectionSelection details
Rfree0.1872 2349 5.1 %RANDOM
Rwork0.1522 ---
obs0.154 46346 97.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 50.8 Å2 / Biso mean: 15.2051 Å2 / Biso min: 3.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å2-0.53 Å2-0.26 Å2
2--0.27 Å20.13 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.402 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3383 0 100 556 4039
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223691
X-RAY DIFFRACTIONr_bond_other_d0.0010.022528
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.9715006
X-RAY DIFFRACTIONr_angle_other_deg0.90836159
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9985487
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70123.929168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.43615588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5021529
X-RAY DIFFRACTIONr_chiral_restr0.10.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214141
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02737
X-RAY DIFFRACTIONr_mcbond_it0.7771.52269
X-RAY DIFFRACTIONr_mcbond_other0.2281.5929
X-RAY DIFFRACTIONr_mcangle_it1.35723681
X-RAY DIFFRACTIONr_scbond_it2.33631422
X-RAY DIFFRACTIONr_scangle_it3.7374.51302
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 158 -
Rwork0.216 3222 -
all-3380 -
obs--95.78 %
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)
10.87970.24180.2250.69810.2030.4419-0.02670.04730.0090.01680.0004-0.01710.00030.0190.02630.00920.0040.01150.02370.01130.033351.3725.98523.974
20.69260.03270.0560.61350.18050.5391-0.00540.01770.0053-0.0146-0.0120.0132-0.00690.00890.01740.00710.00610.00810.00990.00890.036561.26511.13755.107
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 221
2X-RAY DIFFRACTION2B0 - 221

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