1I5Z

STRUCTURE OF CRP-CAMP AT 1.9 A

> Summary

Summary for 1I5Z

Related1G6N 3GAP
DescriptorCATABOLITE GENE ACTIVATOR PROTEIN
Functional Keywordscamp receptor protein (crp), allostery, dna binding cyclic amp, transcription regulation, catabolite activator protein (cap), dna binding protein
Biological sourceEscherichia coli
Total number of polymer chains2
Total molecular weight48314.73
Authors
White, M.A.,Lee, J.C.,Fox, R.O. (deposition date: 2001-03-01, release date: 2003-06-17, modification date: 2009-02-24)
Primary citation
White, M.A.,Liu, D.,Lin, S.-H.,Fox, R.O.,Lee, J.C.
The effect of the D53H point mutation on the macroscopic motions of E. coli Cyclic AMP Receptor Protein
To be Published,
Experimental method
X-RAY DIFFRACTION (1.9 Å)
NMR Information
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.2391001.7%7.6%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 1i5z
no rotation
Molmil generated image of 1i5z
rotated about x axis by 90°
Molmil generated image of 1i5z
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, BCATABOLITE GENE ACTIVATOR PROTEINpolymer20923541.42
UniProt (P0ACJ8)
Pfam (PF00027)
Pfam (PF00325)
Escherichia coli@PDBjCAMP RECEPTOR PROTEIN, CRP, CAP
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOLnon-polymer122.12
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATEnon-polymer329.23
waterwater18.0252

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight47082.8
Non-Polymers*Number of molecules5
Total molecular weight1231.9
All*Total molecular weight48314.7
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.9 Å)

Cell axes46.02893.024105.503
Cell angles90.0090.0090.00
SpacegroupP 21 21 21
Resolution limits46.51 - 1.90
the highest resolution shell value1.930 - 1.900
R-work0.21500
the highest resolution shell value0.293
R-free0.24200
the highest resolution shell value0.332
RMSD bond length0.006
RMSD bond angle1.200

Data Collection Statistics

Resolution limits50.00 - 1.90
the highest resolution shell value -
Number of reflections38852
Rmerge_l_obs0.050
the highest resolution shell value0.270
Completeness99.9
Redundancy4.4
the highest resolution shell value4.2
I/sigma(I)0

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1LIQUID DIFFUSION7.8298

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0005829cellular_componentcytosol
A0030552molecular_functioncAMP binding
A0003677molecular_functionDNA binding
A0003700molecular_functiontranscription factor activity, sequence-specific DNA binding
A0045013biological_processcarbon catabolite repression of transcription
A0045892biological_processnegative regulation of transcription, DNA-templated
A0045893biological_processpositive regulation of transcription, DNA-templated
A0006351biological_processtranscription, DNA-templated
B0005829cellular_componentcytosol
B0030552molecular_functioncAMP binding
B0003677molecular_functionDNA binding
B0003700molecular_functiontranscription factor activity, sequence-specific DNA binding
B0045013biological_processcarbon catabolite repression of transcription
B0045892biological_processnegative regulation of transcription, DNA-templated
B0045893biological_processpositive regulation of transcription, DNA-templated
B0006351biological_processtranscription, DNA-templated
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC13BINDING SITE FOR RESIDUE TRS A 351
ChainResidue
ATRP13
AASN109
BASP138

AC26BINDING SITE FOR RESIDUE TRS A 352
ChainResidue
ALYS130
AASN133
ALEU134
AARG142
ATHR146
AILE175

AC314BINDING SITE FOR RESIDUE CMP A 301
ChainResidue
AVAL49
ALEU61
AILE70
AGLY71
AGLU72
ALEU73
AARG82
ASER83
AARG123
ATHR127
AHOH553
AHOH627
BLEU124
BSER128

AC413BINDING SITE FOR RESIDUE CMP A 302
ChainResidue
ALYS57
AGLU58
AGLN170
AGLY173
AGLN174
AGLY177
ACYS178
ASER179
AARG180
AHOH526
AHOH667
BALA135
BPHE136

AC515BINDING SITE FOR RESIDUE CMP B 401
ChainResidue
ALEU124
ASER128
AHOH554
BVAL49
BLEU61
BILE70
BGLY71
BGLU72
BLEU73
BARG82
BSER83
BALA84
BTHR127
BHOH542
BHOH546

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
TRS_1i5z_A_35152-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL binding site
ChainResidueligand
APRO9-THR10TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
ATRP13TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
AVAL108-ASN109TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

CMP_1i5z_A_30122ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE binding site
ChainResidueligand
AILE30CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
AALA36CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
AVAL49CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
ALEU61-SER62CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
ALEU64CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
APHE69-GLY74CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
AGLU81-ALA84CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
AVAL86CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
ATYR99CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
AARG123CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
ATHR127CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
BLEU124CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
BSER128CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE

CMP_1i5z_A_30214ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE binding site
ChainResidueligand
AGLY56-MET59CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
AARG169-GLN170CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
AGLY173-GLN174CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
AGLY177-ARG180CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
BALA135-PHE136CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE

CMP_1i5z_B_40122ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE binding site
ChainResidueligand
ALEU124CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
ASER128CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
BILE30CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
BALA36CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
BVAL49CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
BLEU61-SER62CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
BLEU64CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
BPHE69-GLY74CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
BGLU81-ALA84CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
BVAL86CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
BTYR99CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
BARG123CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
BTHR127CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE

TRS_1i5z_A_352112-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL binding site
ChainResidueligand
ALYS130TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
AASN133-LEU134TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
AGLY141-ILE143TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
AGLN145-THR146TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
AASN149TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
AILE175-VAL176TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
PS000422Crp-type HTH domain signature. [LIVM]-[STAG]-[RHNWM]-x(2)-[LIM]-[GA]-x-[LIVMFYAS]-[LIVSC]-[GA]-x
ChainResidueDetails
ANA*
BNA*

PS008892Cyclic nucleotide-binding domain signature 2. [LIVMF]-G-E-x-[GAS]-[LIVM]-x(5,11)-R-[STAQ]-A-x-[LIVMA]-x-[STACV]
ChainResidueDetails
ANA*
BNA*

PS008882Cyclic nucleotide-binding domain signature 1. [LIVM]-[VIC]-x-{H}-G-[DENQTA]-x-[GAC]-{L}-x-[LIVMFY](4)-x(2)-G
ChainResidueDetails
ANA*
BNA*

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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI11cAMP.
ChainResidueDetails
ASER128

SWS_FT_FI21H-T-H motif.
ChainResidueDetails
ANA*

SWS_FT_FI31cAMP.
ChainResidueDetails
ANA*

SWS_FT_FI41cAMP.
ChainResidueDetails
BSER128

SWS_FT_FI51H-T-H motif.
ChainResidueDetails
BNA*

SWS_FT_FI61cAMP.
ChainResidueDetails
BNA*

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Catalytic Information from CSA

site_idNumber of ResiduesDetails
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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

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