Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF MARR/EMRR FAMILY TRANSCRIPTIONAL REGULATOR FROM ACINETOBACTER SP. ADP1
 
Authors :  R. Zhang, R. Wu, A. Joachimiak, Midwest Center For Structural Geno (Mcsg)
Date :  30 Jun 10  (Deposition) - 15 Sep 10  (Release) - 15 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Transcriptional Regulator, Psi-2, Protein Structure Initiative, Structural Genomics, Midwest Center For Structural Genomics (Mcsg), Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Rongguang, W. Ruiying, J. Andrzej, Midwest Center For Structural Genomics (Mcsg)
Crystal Strucutre Of Marr/Emrr Family Transcriptional Regulator From Acinetobacter Sp. Adp1
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE TRANSCRIPTIONAL REGULATOR (MARR/EMRR FAMILY)
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PDM68
    Gene: 2878967, ACIAD1811
    Organism Scientific: ACINETOBACTER SP. ADP1
    Organism Taxid: 62977

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 32)

Asymmetric Unit (4, 32)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MSE20Mod. Amino AcidSELENOMETHIONINE
3NA1Ligand/IonSODIUM ION
4SO47Ligand/IonSULFATE ION
Biological Unit 1 (3, 17)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE10Mod. Amino AcidSELENOMETHIONINE
3NA-1Ligand/IonSODIUM ION
4SO45Ligand/IonSULFATE ION
Biological Unit 2 (3, 14)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE10Mod. Amino AcidSELENOMETHIONINE
3NA-1Ligand/IonSODIUM ION
4SO42Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:49 , SER A:50 , HOH A:396 , LYS C:20 , HOH C:165BINDING SITE FOR RESIDUE SO4 A 146
02AC2SOFTWARELYS A:24 , TYR A:29 , MSE A:37 , GOL A:149BINDING SITE FOR RESIDUE SO4 A 147
03AC3SOFTWAREMSE A:22 , ARG A:41 , SER A:44 , LEU A:61 , HOH A:161 , HOH A:483 , HOH A:494 , ASN C:15 , ASN C:19 , MSE C:22BINDING SITE FOR RESIDUE GOL A 148
04AC4SOFTWARETHR A:30 , TRP A:40 , ALA A:112 , SO4 A:147 , HOH A:156 , HOH A:171 , HIS C:9BINDING SITE FOR RESIDUE GOL A 149
05AC5SOFTWAREPHE B:33 , TYR B:80 , GLY C:85 , TYR C:93 , HOH C:393BINDING SITE FOR RESIDUE NA B 146
06AC6SOFTWAREMSE B:22 , ARG B:41 , SER B:44 , LEU B:61 , HOH B:157 , HOH B:445 , ASN D:15 , ASN D:19 , MSE D:22BINDING SITE FOR RESIDUE GOL B 147
07AC7SOFTWARETHR B:38 , ARG B:41 , HOH B:482 , ASP D:64 , HOH D:176BINDING SITE FOR RESIDUE GOL B 148
08AC8SOFTWAREASP A:64 , LYS A:65 , ARG C:70 , LYS C:74BINDING SITE FOR RESIDUE SO4 C 146
09AC9SOFTWAREGLU A:125 , LYS A:128 , ARG C:8BINDING SITE FOR RESIDUE SO4 C 147
10BC1SOFTWARESER C:50 , ASP C:51 , HIS C:86 , ARG C:91 , ALA C:94 , ASN C:96 , HOH C:170BINDING SITE FOR RESIDUE SO4 C 148
11BC2SOFTWAREALA B:49 , SER B:50 , LYS D:20BINDING SITE FOR RESIDUE SO4 D 146
12BC3SOFTWAREASP B:64 , LYS B:65 , ARG D:70 , LYS D:74BINDING SITE FOR RESIDUE SO4 D 147

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NRV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NRV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NRV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NRV)

(-) Exons   (0, 0)

(no "Exon" information available for 3NRV)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:131
 aligned with Q6FBB7_ACIAD | Q6FBB7 from UniProtKB/TrEMBL  Length:145

    Alignment length:144
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141    
         Q6FBB7_ACIAD     2 QKINIDRHATAQINMLANKLMLKSSTAYTQKFGIGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYEVASDFAIEREKQLLEEFEEAEKDQLFILLKKLRNKVDQM 145
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhh----.hhhhh.hhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..ee.---------...eehhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3nrv A   2 QKINIDRHATAQINmLANKLmLK----YTQKFGIGmTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEV---------YAINLTEmGQELYEVASDFAIEREKQLLEEFEEAEKDQLFILLKKLRNKVDQm 145
                                    11    |   21| |    |31     |  41        51        61        71        81 |       - |     101       111       121       131       141   |
                                         16-MSE | |   29      37-MSE                                        83        93      |                                          145-MSE
                                               22-MSE                                                                       100-MSE                                         
                                                 24                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:130
 aligned with Q6FBB7_ACIAD | Q6FBB7 from UniProtKB/TrEMBL  Length:145

    Alignment length:144
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141    
         Q6FBB7_ACIAD     2 QKINIDRHATAQINMLANKLMLKSSTAYTQKFGIGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYEVASDFAIEREKQLLEEFEEAEKDQLFILLKKLRNKVDQM 145
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh-----.hhhhh.hhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..ee.---------...eehhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3nrv B   2 QKINIDRHATAQINmLANKLmL-----YTQKFGIGmTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEV---------YAINLTEmGQELYEVASDFAIEREKQLLEEFEEAEKDQLFILLKKLRNKVDQm 145
                                    11    |   21||     |31     |  41        51        61        71        81 |       - |     101       111       121       131       141   |
                                         16-MSE ||    29      37-MSE                                        83        93      |                                          145-MSE
                                               22-MSE                                                                       100-MSE                                         
                                                23                                                                                                                          


Chain C from PDB  Type:PROTEIN  Length:142
 aligned with Q6FBB7_ACIAD | Q6FBB7 from UniProtKB/TrEMBL  Length:145

    Alignment length:142
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143  
         Q6FBB7_ACIAD     4 INIDRHATAQINMLANKLMLKSSTAYTQKFGIGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYEVASDFAIEREKQLLEEFEEAEKDQLFILLKKLRNKVDQM 145
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee.........eeeehhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nrv C   4 INIDRHATAQINmLANKLmLKSSTAYTQKFGIGmTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEmGQELYEVASDFAIEREKQLLEEFEEAEKDQLFILLKKLRNKVDQm 145
                                    13  |     23        33   |    43        53        63        73        83        93      |103       113       123       133       143 |
                                       16-MSE |             37-MSE                                                        100-MSE                                      145-MSE
                                             22-MSE                                                                                                                       


Chain D from PDB  Type:PROTEIN  Length:142
 aligned with Q6FBB7_ACIAD | Q6FBB7 from UniProtKB/TrEMBL  Length:145

    Alignment length:142
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143  
         Q6FBB7_ACIAD     4 INIDRHATAQINMLANKLMLKSSTAYTQKFGIGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYEVASDFAIEREKQLLEEFEEAEKDQLFILLKKLRNKVDQM 145
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------MarR-3nrvD01 D:35-93                                       ---------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------MarR-3nrvD02 D:35-93                                       ---------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -------------------------------MarR-3nrvD03 D:35-93                                       ---------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -------------------------------MarR-3nrvD04 D:35-93                                       ---------------------------------------------------- Pfam domains (4)
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee.........eeeehhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nrv D   4 INIDRHATAQINmLANKLmLKSSTAYTQKFGIGmTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEmGQELYEVASDFAIEREKQLLEEFEEAEKDQLFILLKKLRNKVDQm 145
                                    13  |     23        33   |    43        53        63        73        83        93      |103       113       123       133       143 |
                                       16-MSE |             37-MSE                                                        100-MSE                                      145-MSE
                                             22-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3NRV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NRV)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q6FBB7_ACIAD | Q6FBB7)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3nrv)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3nrv
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q6FBB7_ACIAD | Q6FBB7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q6FBB7_ACIAD | Q6FBB7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 3NRV)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3NRV)