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- PDB-3mzh: Crystal structure of cAMP receptor protein from mycobacterium tub... -

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Basic information

Entry
Database: PDB / ID: 3mzh
TitleCrystal structure of cAMP receptor protein from mycobacterium tuberculosis in complex with cAMP and its DNA binding element
Components
  • 5'-D(P*AP*AP*AP*TP*GP*TP*GP*AP*TP*CP*TP*AP*GP*GP*TP*CP*AP*CP*GP*TP*G)-3'
  • 5'-D(P*CP*AP*CP*GP*TP*GP*AP*CP*CP*TP*AP*GP*AP*TP*CP*AP*CP*AP*TP*C)-3'
  • PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY CRP/FNR-FAMILY)
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION / TRANSCRIPTION REGULATOR / CAMP / CAMP RECEPTOR PROTEIN / CRP / RV3676 / DNA-BINDING / TRANSCRIPTION REGULATION / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


cell wall / cAMP binding / peptidoglycan-based cell wall / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / plasma membrane / cytosol
Similarity search - Function
helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls ...helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Jelly Rolls / Winged helix-like DNA-binding domain superfamily / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / DNA / DNA (> 10) / CRP-like cAMP-activated global transcriptional regulator / CRP-like cAMP-activated global transcriptional regulator
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsAkhter, Y. / Wilmanns, M.
CitationJournal: To be Published
Title: Crystal Structure of Camp Receptor Protein from Mycobacterium Tuberculosis in Complex with DNA and cAMP
Authors: Akhter, Y. / Pogenberg, V. / Hasnain, S.E. / Wilmanns, M.
History
DepositionMay 12, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Other
Revision 1.3Nov 1, 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_ncs_dom_lim / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY CRP/FNR-FAMILY)
B: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY CRP/FNR-FAMILY)
C: 5'-D(P*AP*AP*AP*TP*GP*TP*GP*AP*TP*CP*TP*AP*GP*GP*TP*CP*AP*CP*GP*TP*G)-3'
D: 5'-D(P*CP*AP*CP*GP*TP*GP*AP*CP*CP*TP*AP*GP*AP*TP*CP*AP*CP*AP*TP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4827
Polymers62,4944
Non-polymers9883
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7740 Å2
ΔGint-54 kcal/mol
Surface area25560 Å2
Unit cell
Length a, b, c (Å)66.130, 61.250, 89.940
Angle α, β, γ (deg.)90.00, 104.29, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETSERSERchain A and (resseq 1:17 or resseq 20:224 )AA1 - 172 - 18
12ALAALAARGARGchain A and (resseq 1:17 or resseq 20:224 )AA20 - 22421 - 225
21METMETSERSERchain B and (resseq 1:17 or resseq 20:224 )BB1 - 172 - 18
22ALAALAARGARGchain B and (resseq 1:17 or resseq 20:224 )BB20 - 22421 - 225

NCS oper: (Code: given
Matrix: (-0.999982, -0.004337, 0.004229), (0.004355, -0.999981, 0.004313), (0.004211, 0.004332, 0.999982)
Vector: -10.7175, -24.1399, 0.048219)

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Components

#1: Protein PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY CRP/FNR-FAMILY) / CRP / Transcriptional regulator / Crp/Fnr family


Mass: 24964.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv3676 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O69644, UniProt: P9WMH3*PLUS
#2: DNA chain 5'-D(P*AP*AP*AP*TP*GP*TP*GP*AP*TP*CP*TP*AP*GP*GP*TP*CP*AP*CP*GP*TP*G)-3'


Mass: 6502.220 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(P*CP*AP*CP*GP*TP*GP*AP*CP*CP*TP*AP*GP*AP*TP*CP*AP*CP*AP*TP*C)-3'


Mass: 6062.944 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP / Cyclic adenosine monophosphate


Mass: 329.206 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H12N5O6P

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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: 2.78 Å3/Da / Density % sol: 55.73 % / Mosaicity: 1.03 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M MAGNESIUM CHLORIDE, 0.1M TRIS-CL pH 8.5, 30%(W/V) PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0066 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2008
RadiationMonochromator: Single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0066 Å / Relative weight: 1
ReflectionResolution: 2.9→44.278 Å / Num. all: 14717 / Num. obs: 14717 / % possible obs: 94.1 % / Redundancy: 2.2 % / Rpim(I) all: 0.083 / Rrim(I) all: 0.136 / Rsym value: 0.106 / Net I/av σ(I): 4.279 / Net I/σ(I): 5.1 / Num. measured all: 32355
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.9-3.062.20.4550.3532.1477321500.2840.4550.3532.295.3
3.06-3.242.20.2750.2162.6454520500.1680.2750.2163.195.6
3.24-3.472.20.190.152.5432019390.1150.190.154.295.5
3.47-3.742.20.170.1344.7392917750.1030.170.1345.194.1
3.74-4.12.20.1250.0985.7359916430.0760.1250.0986.194.8
4.1-4.592.20.1160.0916320114530.070.1160.091793.2
4.59-5.292.20.0920.0728.4282812890.0560.0920.0727.192.2
5.29-6.482.10.0980.0776.8225710750.060.0980.0776.690.9
6.48-9.172.10.0780.0617.518088560.0470.0780.0617.793.1
9.17-44.2782.20.0940.0736.210954870.0580.0940.0738.992

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Processing

Software
NameVersionClassification
DNAdata collection
Auto-Rickshawphasing
PHASERphasing
PHENIX1.6.1_357refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GAU

2gau


Resolution: 2.9→43.579 Å / Occupancy max: 1 / Occupancy min: 0.38 / SU ML: 0.45 / Cross valid method: Rfree / σ(F): 0.06 / Phase error: 29.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.279 705 4.97 %Rfree was calculated using 6.54% of data, which was omitted from the refinement
Rwork0.2467 13477 --
obs0.2482 14182 90.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.73 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso max: 253.02 Å2 / Biso mean: 65.1967 Å2 / Biso min: 8.7 Å2
Baniso -1Baniso -2Baniso -3
1--5.4172 Å20 Å2-1.1224 Å2
2--13.9816 Å20 Å2
3----8.5645 Å2
Refinement stepCycle: LAST / Resolution: 2.9→43.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3432 840 66 0 4338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124472
X-RAY DIFFRACTIONf_angle_d1.4656244
X-RAY DIFFRACTIONf_dihedral_angle_d23.8571728
X-RAY DIFFRACTIONf_chiral_restr0.07722
X-RAY DIFFRACTIONf_plane_restr0.01660
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1615X-RAY DIFFRACTIONPOSITIONAL0.602
12B1615X-RAY DIFFRACTIONPOSITIONAL0.602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.12390.39561320.34392532X-RAY DIFFRACTION86
3.1239-3.43810.30771380.28182670X-RAY DIFFRACTION90
3.4381-3.93530.28021520.24432749X-RAY DIFFRACTION93
3.9353-4.9570.2321330.20562764X-RAY DIFFRACTION92
4.957-43.58360.25441500.22372762X-RAY DIFFRACTION91
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)
10.86780.47710.22330.77320.16860.23550.59280.18160.2175-0.9362-0.58880.1822-0.0814-0.38460.1773-0.286-0.192-0.28870.0124-0.09820.2105-21.3337-13.5565-37.4638
22.55490.10540.51970.38210.73022.0792-0.0185-0.76880.7991-0.1791-0.0368-0.0242-0.4684-0.05480.37240.07690.0203-0.07370.148-0.11260.3264-15.7792-2.1542-23.7718
30.476-0.03470.54380.63680.09920.75940.13420.0879-0.1136-0.3563-0.1384-0.114-0.00860.43710.1192-0.1061-0.03040.00440.09740.00510.216510.2384-10.4993-37.5275
41.54950.2734-0.20440.0939-0.52681.8994-0.0261-1.1088-0.3874-0.4122-0.06670.121.0265-0.1603-0.14-0.0839-0.0643-0.0234-0.09580.13160.23335.0419-22.4125-23.2495
53.5887-0.80.22911.41-0.19690.4347-0.4719-1.4210.48790.06370.06440.40440.0151-0.3483-0.18130.1405-0.1249-0.07171.0398-0.27870.4017-13.6727-10.7135-2.3792
61.1131-0.1803-0.11150.0802-0.07760.1519-0.02040.28290.026-0.11160.2574-0.48250.2822-0.0443-0.04340.2346-0.1242-0.27191.77350.06790.835322.077-14.7359-0.569
72.3717-0.64440.30442.03860.26860.2882-0.5738-1.5933-0.01120.51510.2299-0.11410.01520.6193-0.04110.1008-0.1161-0.16561.13210.12790.42761.3913-13.3423-1.9783
81.60190.2321.15882.24350.26454.1191-0.924-0.3779-0.4656-0.39360.04870.2410.0555-0.13390.37490.0664-0.18760.07261.240.03120.6048-32.3651-9.0943-0.1579
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 0:107)A0 - 107
2X-RAY DIFFRACTION2(chain A and resid 108:224)A108 - 224
3X-RAY DIFFRACTION3(chain B and resid 0:110)B0 - 110
4X-RAY DIFFRACTION4(chain B and resid 111:224)B111 - 224
5X-RAY DIFFRACTION5(chain C and resid 3:19)C3 - 19
6X-RAY DIFFRACTION6(chain C and resid 20:23)C20 - 23
7X-RAY DIFFRACTION7(chain D and resid 3:18)D3 - 18
8X-RAY DIFFRACTION8(chain D and resid 19:22)D19 - 22

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