2GHY

Novel Crystal Form of the ColE1 Rom Protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Novel crystal form of the ColE1 Rom protein.

Jang, S.B.Jeong, M.S.Carter, R.J.Holbrook, E.L.Comolli, L.R.Holbrook, S.R.

(2006) Acta Crystallogr D Biol Crystallogr 62: 619-627

  • DOI: 10.1107/S0907444906012388
  • Primary Citation of Related Structures:  
    2GHY

  • PubMed Abstract: 
  • The RNA I modulator protein (Rom) acts as a co-regulator of ColE1 plasmid copy number by binding to RNA kissing hairpins and stabilizing their interaction. The structure of Rom has been determined in a new crystal form from X-ray diffraction data to ...

    The RNA I modulator protein (Rom) acts as a co-regulator of ColE1 plasmid copy number by binding to RNA kissing hairpins and stabilizing their interaction. The structure of Rom has been determined in a new crystal form from X-ray diffraction data to 2.5 A resolution. In this structure, a dimer of the 57-amino-acid protein is found in the asymmetric unit. Each subunit consists almost entirely of two antiparallel alpha-helices joined by a short hairpin bend. The dimer contains a non-crystallographic twofold axis and forms a highly regular four-alpha-helical bundle. The structural packing in this novel crystal form is different from previously known Rom structures. The asymmetric unit contains one dimer, giving a crystal volume per protein weight (V(M)) of 1.83 A(3) Da(-1) and a low solvent content of 30%. Strong packing interactions and low solvation are characteristic of the structure. The Rom protein was cocrystallized with the Tar-Tar* kissing hairpin RNA. Although the electron-density maps do not show bound RNA, altered conformations in the side chains of Rom that are known to be involved in RNA binding have been identified. These results provide additional information about Rom protein conformational flexibility and suggest that the presence of a highly charged polymer such as RNA can promote tight packing of an RNA-binding protein, even when the RNA itself is not observed in the crystal.


    Organizational Affiliation

    Korea Nanobiotechnology Center, Pusan National University, Jangjeon-dong, Keumjeong-gu, Busan 609-735, South Korea. sbjang@pusan.ac.kr



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Regulatory protein ropAB63Escherichia coliMutation(s): 0 
Gene Names: 
ropromrop_1rop_2rop_3BB545_22150BMA87_25550BvCmsC61A_05221BvCmsHHP001_05195BvCmsKKP061_05282BvCmsKSNP073_05823BvCmsKSNP081_05222BvCmsKSNP120_05137BvCmsSINP011_05221BvCmsSIP019_05380BWI89_28350C4M78_27450C5715_28160C7B08_27315C9160_27110C9E25_27725CRT43_28510CRX46_26705CSB64_13720CWM24_08555D0X26_29450D2184_28075D3P02_25155D3Y67_32715D4718_24025D6C36_25995D9C02_26580D9D33_25675D9D43_28005D9D94_25555D9G42_24610D9H53_24920D9I87_26910D9J11_25835D9K48_03015D9K48_14435DAH26_28415DD762_27200DK132_24755DL326_26450DLY44_24920DM267_24845DM973_27325DTL43_26080DTZ20_28325E0L12_25810E2127_25875E2128_17330E5P24_23830E5S62_23795EA191_28300EA239_25735EA250_26655EA429_26250EF082_27375EG075_24630EI028_25480EI041_23190EPS91_26280EPS91_26880EQ830_26515ERS085366_04862ERS085411_04699EYX82_23150EYX82_23450EYY34_00560F9225_23965FY127_24910G5670_27430G5697_24190GFU40_24935GKF89_24310GQA63_25160GQA64_25115GQE33_24095GQE33_24200GQE33_24320GQE34_26700GQE51_24575GQE51_24950GQF59_25135GQY14_25960GUC40_24205GUI16_24220GZS12_25950HUS41_pIII0001NCTC10082_05556NCTC10090_04840NCTC9045_06076RCS76_PIICDS5798DRCS83_PIII0002SAMEA3472043_04975SAMEA3472070_05337SAMEA3472080_05366SAMEA3472090_05190SAMEA3472090_05194SAMEA3472110_05822SAMEA3472112_05909SAMEA3472114_05350SAMEA3752372_05881SAMEA3752557_05352SAMEA3752557_05360SAMEA3752559_05022SAMEA3752559_05030SAMEA3752620_04898SAMEA3753064_05634SAMEA3753164_04925SAMEA3753290_05644SAMEA3753300_04208

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Go to UniProtKB:  P03051
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Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.77α = 90
b = 39.11β = 96.16
c = 26.7γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-05-30
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance