1QAR - Header Asymmetric Unit

HEADER PROTEIN/DNA 22-MAR-99 1QAR

TITLE P22 C2 REPRESSOR DIMER MODEL BOUND TO OPERATOR DNA

COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(P*AP*TP*TP*TP*AP*AP*GP*AP*CP*TP*TP*CP*TP*TP*AP*AP*TP*T)- COMPND 4 3'); COMPND 5 CHAIN: A; COMPND 6 SYNONYM: OPERATOR SITE OL1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'- COMPND 10 D(P*AP*AP*TP*TP*AP*AP*GP*AP*AP*GP*TP*CP*TP*TP*AP*AP*AP*T)- COMPND 11 3'); COMPND 12 CHAIN: B; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: PROTEIN (BACTERIOPHAGE P22 REPRESSOR); COMPND 16 CHAIN: C, D; COMPND 17 FRAGMENT: RESIDUES 1-216

SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_COMMON: BACTERIOPHAGE P22

KEYWDS FULL P22 REPRESSOR, GENE REGULATION, OPERATOR SITES

EXPDTA THEORETICAL MODEL

AUTHOR R.CHATTOPADHYAYA,K.GHOSH

REVDAT 1 23-MAR-99 1QAR 0

JRNL AUTH R.CHATTOPADHYAYA,K.GHOSH JRNL TITL THE COMMON THREE DIMENSIONAL STRUCTURE OF THE JRNL TITL 2 CARBOXY TERMINAL DOMAINS OF LAMBDA, P22 AND 434 JRNL TITL 3 REPRESSORS JRNL REF TO BE PUBLISHED JRNL REFN

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.SEVILLA-SIERRA,G.OTTING,K.WUTHRICH REMARK 1 TITL DETERMINATION OF THE NUCLEAR MAGNETIC RESONANCE REMARK 1 TITL 2 STRUCTURE OF THE DNA-BINDING DOMAIN OF THE P22 C2 REMARK 1 TITL 3 REPRESSOR (1 TO 76) IN SOLUTION AND COMPARISON REMARK 1 TITL 4 WITH THE DNA-BINDING DOMAIN OF THE 434 REPRESSOR REMARK 1 REF J.MOL.BIOL. V. 235 1003 1994 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH L.W.SHIMON,S.C.HARRISON REMARK 1 TITL THE PHAGE 434 OR2(SLASH(R1-69 COMPLEX AT 2.5 REMARK 1 TITL 2 ANGSTROMS RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 232 826 1993 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REFERENCE 3 REMARK 1 AUTH R.T.SAUER,R.R.YOCUM,R.F.DOOLITTLE,M.LEWIS,C.O.PABO REMARK 1 TITL HOMOLOGY AMONG DNA-BINDING PROTEINS SUGGESTS USE REMARK 1 TITL 2 OF A CONSERVED SUPER-SECONDARY STRUCTURE REMARK 1 REF NATURE V. 298 447 1982 REMARK 1 REFN ASTM NATUAS UK ISSN 0028-0836 REMARK 1 REFERENCE 4 REMARK 1 AUTH R.T.SAUER,S.R.JORDAN,C.O.PABO REMARK 1 TITL LAMBDA REPRESSOR : A MODEL SYSTEM FOR REMARK 1 TITL 2 UNDERSTANDING PROTEIN-DNA INTERACTIONS AND PROTEIN REMARK 1 TITL 3 STABILITY REMARK 1 REF ADV.PROTEIN CHEM. V. 40 1 1990 REMARK 1 REFN ASTM APCHA2 US ISSN 0065-3233 REMARK 1 REFERENCE 5 REMARK 1 AUTH U.BANIK,R.SAHA,N.C.MANDAL,B.BHATTACHARYYA,S.ROY REMARK 1 TITL MULTIPHASIC DENATURATION OF THE LAMBDA REPRESSOR REMARK 1 TITL 2 BY UREA AND ITS IMPLICATIONS FOR THE REPRESSOR REMARK 1 TITL 3 STRUCTURE REMARK 1 REF EUR.J.BIOCHEM. V. 206 15 1992 REMARK 1 REFN ASTM EJBCAI IX ISSN 0014-2956 REMARK 1 REFERENCE 6 REMARK 1 AUTH J.DEANDA,A.R.POTEETE,R.T.SAUER REMARK 1 TITL P22 C2 REPRESSOR DOMAIN STRUCTURE AND FUNCTION REMARK 1 REF J.BIOL.CHEM. V. 258 10536 1983 REMARK 1 REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 1 REFERENCE 7 REMARK 1 AUTH D.VALENZUELA,M.PTASHNE REMARK 1 TITL P22 REPRESSOR MUTANTS DEFICIENT IN COOPERATIVE REMARK 1 TITL 2 BINDING AND DNA LOOP FORMATION REMARK 1 REF EMBO J. V. 8 4345 1989 REMARK 1 REFN ASTM EMJODG UK ISSN 0261-4189 REMARK 1 REFERENCE 8 REMARK 1 AUTH C.WEBSTER,A.MERRYWEATHER,W.BRAMMAR REMARK 1 TITL EFFICIENT REPRESSION BY A HETERODIMERIC REPRESSOR REMARK 1 TITL 2 IN ESCHERICHIA COLI REMARK 1 REF MOL.MICROBIOL. V. 6 371 1992 REMARK 1 REFN ASTM MOMIEE UK ISSN 0950-382X REMARK 1 REFERENCE 9 REMARK 1 AUTH P.A.CARLSON,G.B.KOUDELKA REMARK 1 TITL EXPRESSION, PURIFICATION, AND FUNCTIONAL REMARK 1 TITL 2 CHARACTERIZATION OF THE CARBOXYL-TERMINAL DOMAIN REMARK 1 TITL 3 FRAGMENT OF BACTERIOPHAGE 434 REPRESSOR REMARK 1 REF J.BACTERIOL. V. 176 6907 1994 REMARK 1 REFN ASTM JOBAAY US ISSN 0021-9193 REMARK 1 REFERENCE 10 REMARK 1 AUTH A.L.DONNER,P.A.CARLSON,G.B.KOUDELKA REMARK 1 TITL DIMERIZATION SPECIFICITY OF P22 AND 434 REPRESSORS REMARK 1 TITL 2 IS DETERMINED BY MULTIPLE POLYPEPTIDE SEGMENTS REMARK 1 REF J.BACTERIOL. V. 179 1253 1997 REMARK 1 REFN ASTM JOBAAY US ISSN 0021-9193 REMARK 1 REFERENCE 11 REMARK 1 AUTH F.W.WHIPPLE,N.H.KULDELL,L.A.CHEATHAM,A.HOCHSCHILD REMARK 1 TITL SPECIFICITY DETERMINANTS FOR THE INTERACTION OF REMARK 1 TITL 2 LAMBDA REPRESSOR AND P22 REPRESSOR DIMERS REMARK 1 REF GENES DEV. V. 8 1212 1994 REMARK 1 REFN ASTM GEDEEP US ISSN 0890-9369 REMARK 1 REFERENCE 12 REMARK 1 AUTH F.W.WHIPPLE,E.F.HOU,A.HOCHSCHILD REMARK 1 TITL AMINO ACID-AMINO ACID CONTACTS AT THE REMARK 1 TITL 2 COOPERATIVITY INTERFACE OF THE BACTERIOPHAGE REMARK 1 TITL 3 LAMBDA AND P22 REPRESSORS REMARK 1 REF GENES DEV. V. 12 2791 1998 REMARK 1 REFN ASTM GEDEEP US ISSN 0890-9369 REMARK 1 REFERENCE 13 REMARK 1 AUTH M.HOLLIS,D.VALENZUELA,D.POILI,R.WHARTON,M.PTASHNE REMARK 1 TITL A REPRESSOR HETERODIMER BINDS TO A CHIMERIC REMARK 1 TITL 2 OPERATOR REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 85 5834 1988 REMARK 1 REFN ASTM PNASA6 US ISSN 0027-8424 REMARK 1 REFERENCE 14 REMARK 1 AUTH S.P.HILCHEY,G.B.KOUDELKA REMARK 1 TITL DNA-BASED LOSS OF SPECIFICITY MUTATIONS EFFECTS OF REMARK 1 TITL 2 DNA SEQUENCE ON THE CONTACTED AND NON-CONTACTED REMARK 1 TITL 3 BASE PREFERENCES OF BACTERIOPHAGE P22 REPRESSOR REMARK 1 REF J.BIOL.CHEM. V. 272 1646 1997 REMARK 1 REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 1 REFERENCE 15 REMARK 1 AUTH D.N.WOOLFSON,P.E.EVANS,E.G.HUTCHINSON,J.M.THORNTON REMARK 1 TITL TOPOLOGICAL AND STEREOCHEMICAL RESTRICTIONS IN REMARK 1 TITL 2 BETA-SANDWICH PROTEIN STRUCTURES REMARK 1 REF PROTEIN ENG. V. 6 461 1993 REMARK 1 REFN ASTM PRENE9 UK ISSN 0269-2139 REMARK 1 REFERENCE 16 REMARK 1 AUTH V.I.LIM REMARK 1 TITL STRUCTURAL PRINCIPLES OF THE GLOBULAR ORGANIZATION REMARK 1 TITL 2 OF PROTEIN CHAINS. A STEREOCHEMICAL THEORY OF REMARK 1 TITL 3 GLOBULAR PROTEIN STRUCTURE REMARK 1 REF J.MOL.BIOL. V. 88 857 1974 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REFERENCE 17 REMARK 1 AUTH G.GHOSH,G.VAN DUYNE,S.GHOSH,P.B.SIGLER REMARK 1 TITL STRUCTURE OF NF-KB P50 HOMODIMER BOUND TO A KB SITE REMARK 1 REF NATURE V. 373 303 1995 REMARK 1 REFN ASTM NATUAS UK ISSN 0028-0836 REMARK 1 REFERENCE 18 REMARK 1 AUTH T.S.PEAT,E.G.FRANK,J.P.MCDONALD,A.S.LEVINE, REMARK 1 AUTH 2 R.WOODGATE,W.A.HENDRICKSON REMARK 1 TITL STRUCTURE OF THE UMUD' PROTEIN AND ITS REGULATION REMARK 1 TITL 2 IN RESPONSE TO DNA DAMAGE REMARK 1 REF NATURE V. 380 727 1996 REMARK 1 REFN ASTM NATUAS UK ISSN 0028-0836

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 1QAR COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998

REMARK 6 REMARK 6 THE BACTERIOPHAGE P22 C2 REPRESSOR IS A TWO DOMAIN, 216 REMARK 6 RESIDUE REGULATORY PROTEIN. THE N-DOMAIN (1-76), A CHYMO- REMARK 6 TRYPTIC FRAGMENT, BINDS DNA, WHILE THE C-DOMAIN (77-216) IS REMARK 6 INVOLVED IN PROTEIN-PROTEIN CONTACTS. THE P22 REPRESSOR REMARK 6 BINDS TWO SETS OF THREE HOMOLOGOUS, PARTIALLY SYMMETRIC REMARK 6 BINDING SITES (OR1,OR2,OR3,OL1,OL2,OL3) KNOWN AS OPERATOR REMARK 6 SITES. REMARK 6 REMARK 6 THE NMR STRUCTURE OF THE N-DOMAIN (1-76; REF.1 ABOVE) IS REMARK 6 AVAILABLE (PDB CODE 1ADR). REMARK 6 HOWEVER, THE INTACT P22 REPRESSOR OR ANY OF ITS DOMAINS REMARK 6 COULD NOT YET BE STUDIED BY X-RAY CRYSTALLOGRAPHY. REMARK 6 REMARK 6 WE HAVE USED ONE OF THE 20 STRUCTURES IN 1ADR AND FIRST REMARK 6 DOCKED IT ON TO A CONSENSUS OPERATOR SITE FOR P22, SUCH REMARK 6 THAT THE OBSERVED AMINO ACIDS IN THE RECOGNITION HELIX REMARK 6 HAVE FAVORABLE INTERACTIONS WITH THE MAJOR GROOVE, REMARK 6 PARTICULARLY WITH INVARIANT RESIDUES IN P22 OPERATOR REMARK 6 SITES (REF.14). ONCE OPTIMIZED, THIS WAS REPEATED FOR REMARK 6 THE OTHER HALF SITE IN AN IDENTICAL FASHION. REMARK 6 REMARK 6 A1 A18 REMARK 6 REMARK 6 REMARK 6 5'-ATTTAAGACTTCTTAATT-3' OPERATOR OL1 FOR P22 REMARK 6 REMARK 6 REMARK 6 3'-TAAATTCTGAAGAATTAA-5' REMARK 6 B18 B1 REMARK 6 REMARK 6 RESIDUES 1-65 IN OUR P22 MODEL HAVE THE SAME THREE REMARK 6 DIMENSIONAL STRUCTURE AS THE FIRST OF THE 20 STRUCTURES REMARK 6 IN ENTRY 1ADR DETERMINED BY NMR. REMARK 6 REMARK 6 WE HAVE FURTHER EXTENDED THE IDEA IN REF.3 ABOVE TO REMARK 6 CONCLUDE THAT THE C-DOMAINS OF PHAGE REPRESSORS IN REMARK 6 BACTERIOPHAGES LAMBDA, P22 AND 434 POSSESS A COMMON FOLD REMARK 6 AND A COMMON THREE DIMENSIONAL STRUCTURE. THIS HYPOTHESIS REMARK 6 HELPS US TO CORRECTLY PREDICT THE SECONDARY STRUCTURE REMARK 6 COMMON TO ALL THREE ALIGNED REPRESSOR SEQUENCES. WE DO REMARK 6 NOT THINK AT PRESENT THAT THE PHAGE REPRESSORS SHARE THE REMARK 6 REMARK 6 REMARK 6 SAME FOLD WITH LEXA OR UMUD' (CODES 1QAA,1UMU) IN THEIR REMARK 6 C-DOMAINS THOUGH THEY POSSESS SIMILAR SECONDARY STRUCTURE REMARK 6 REMARK 6 PAIRWISE SEQUENCE IDENTITIES BETWEEN THE PHAGE REPRESSOR REMARK 6 C-DOMAINS ARE 35 PER CENT, 45 PER CENT, OR 59 PER CENT REMARK 6 (REF.3) WHEREAS BETWEEN LEXA AND ANY OF THE PHAGES IS REMARK 6 AROUND 21 PER CENT. REMARK 6 REMARK 6 FOUR DIFFERENT OBSERVATIONS WERE CRUCIAL FOR ARRIVING REMARK 6 AT THE CORRECT TOPOLOGY OF THE LAMBDA REP C-DOMAIN REMARK 6 1. ALL THREE CYSTEINE RESIDUES IN CI, NAMELY, REMARK 6 CYS 180, CYS 215 AND CYS 219 ARE UNREACTIVE REMARK 6 (REF.5) AND HENCE, BURIED. REMARK 6 2. AUTOCLEAVAGE INVOLVES LYS 192 AND ALA 111, SO REMARK 6 THEY MUST BE CLOSE TO EACH OTHER REMARK 6 3. AUTOCLEAVAGE INVOLVES SER 149 AND ALA 111, SO REMARK 6 THEY MUST BE CLOSE TO EACH OTHER REMARK 6 4. THE C-DOMAIN IS LARGELY MADE UP OF BETA SHEET REMARK 6 AND INTERVENING LOOPS REMARK 6 REMARK 6 OUR STRATEGY WAS TO BUILD THE C-DOMAIN OF THE P22 C2 REMARK 6 REPRESSOR BY HOMOLOGY USING THE C-DOMAIN OF THE CI REMARK 6 REPRESSOR (MODEL IN RCSB000598 AND 1LMD). HOWEVER, REMARK 6 THE LINKAGE BETWEEN THE TWO DOMAINS IN P22 IS REMARK 6 DIFFERENT FROM THAT IN OUR LAMBDA MODEL(1LMD), AS REMARK 6 WELL AS THE DIMER-DIMER INTERACTION, SINCE P22 HAS REMARK 6 23 BASE STEPS BETWEEN THE CENTERS OF OR1 AND OR2, BUT REMARK 6 LAMBDA HAS 24 BASE STEPS. THE LINKAGE BETWEEN THE REMARK 6 TWO DOMAINS IN P22 IS MORE SIMILAR TO THAT IN 434 REMARK 6 REPRESSOR (RCSB000681,1RPD) THAN WITH LAMBDA (1LMD). REMARK 6 REMARK 6 REMARK 6 REMARK 6 THE UMUD' FOLD IS RULED OUT FOR THE PHAGE REPRESSORS REMARK 6 SINCE, PLACING THE THREE AFOREMENTIONED CYS RESIDUES REMARK 6 IN THAT FOLD EXPOSES THEM TO THE SURFACE, HENCE REMARK 6 THEY SHOULD HAVE BEEN REACTIVE TO NBS2 (REF. 5) REMARK 6 REMARK 6 AS WITH OUR LEXA MODEL, WE PROPOSE THAT NORMALLY REMARK 6 AUTOCLEAVAGE DOES NOT OCCUR AS THE ALA 94 - GLY 95 REMARK 6 IS NOT CLOSE ENOUGH TO THE CATALYTIC GROUPS. IN REMARK 6 P22, THE LYS 174 NZ ATOM IS ABOUT 13 ANGSTROMS AWAY REMARK 6 FROM THE ALA 94 C ATOM. AT ELEVATED PH, OR UNDER REMARK 6 THE ACTIVATION OF RECA, A STRUCTURAL REARRANGEMENT REMARK 6 OCCURS BRINGING THE CATALYTIC GROUPS CLOSER TO REMARK 6 ALA 94 . HOWEVER THE SER 132 OG ATOM IS 4.7 A FROM REMARK 6 THE ALA 94 IN OUR MODEL. IN EFFECT THE STRUCTURAL REMARK 6 REARRANGEMENT MUST BRING ALA 94 C ABOUT 3-4A REMARK 6 FROM BOTH CATALYTIC GROUPS. THIS IS POSSIBLE IN REMARK 6 OUR MODEL BY APPROPRIATELY MOVING BETA1, BETA2 ETC REMARK 6 CLOSER TO LYS 174 NZ, WHILE KEEPING BETA3-BETA8 REMARK 6 FIXED. REMARK 6 REMARK 6 THE VARIOUS MUTAGENESIS STUDIES (REFS.4,7,8,9,10,11, REMARK 6 12 AND MANY MORE) ARE IN GENERAL AGREEMENT WITH OUR REMARK 6 C-DOMAIN MODEL. REMARK 6 REMARK 6 P22 REPRESSOR DIMER FORMATION IS AKIN TO THE REMARK 6 NF-KB DIMER FORMATION (REF.17 ABOVE) IN THAT, THEY REMARK 6 BOTH USE HYDROPHOBIC SIDE CHAINS ON THE EXTERIOR REMARK 6 OF THEIR C-DOMAIN BETA BARRELS, FORMING A PSEUDO REMARK 6 BARREL AT THE MONOMER-MONOMER INTERFACE. REMARK 6 REMARK 6 REMARK 6 IN OUR MODEL, THE REGION 180-192 CONTAINING BETA6 REMARK 6 IS MOST IMPORTANT FOR MAINTAINING COOPERATIVE REMARK 6 OR DIMER-DIMER INTERACTIONS. IT WILL REMARK 6 BE EXPLAINED IN OUR PUBLICATIONS HOW AND WHY THIS REMARK 6 MODEL IS LARGELY CONSISTENT WITH ACCUMULATED REMARK 6 BIOCHEMICAL AND BIOPHYSICAL DATA ABOUT THE LAMBDA, REMARK 6 P22 AND 434 REPRESSORS.

REMARK 7 REMARK 7 MODEL BUILDING FOR THE COMPLETE P22 C2 REPRESSOR REMARK 7 DIMER AND ASSOCIATED OPERATOR DNA WAS CARRIED OUT REMARK 7 USING THE INSIGHT-II PACKAGE INCLUDING PROGRAMS REMARK 7 DISCOVER AND HOMOLOGY

REMARK 8 REMARK 8 THERE ARE TWO P22 REPRESSOR MOLECULES WITH CHAIN REMARK 8 IDENTIFIERS *C*,*D* RESPECTIVELY. OPERATOR REMARK 8 DNA CHAIN IDENTIFIERS *A* AND *B*.

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAR-1999. REMARK 100 THE RCSB ID CODE IS RCSB000693.

REMARK 103 REMARK 103 THERE ARE NON-WATSON-CRICK HYDROGEN BONDS BETWEEN THE REMARK 103 FOLLOWING ATOMS: REMARK 103 N1 A A 1 AND N3 T B 18 REMARK 103 N3 T A 2 AND N1 A B 17 REMARK 103 N3 T A 3 AND N1 A B 16 REMARK 103 N3 T A 4 AND N1 A B 15 REMARK 103 N1 A A 15 AND N3 T B 4 REMARK 103 N1 A A 16 AND N3 T B 3 REMARK 103 N3 T A 17 AND N1 A B 2

REMARK 105 REMARK 105 THE PROTEIN DATA BANK HAS ADOPTED THE SACCHARIDE CHEMISTS REMARK 105 NOMENCLATURE FOR ATOMS OF THE DEOXYRIBOSE/RIBOSE MOIETY REMARK 105 RATHER THAN THAT OF THE NUCLEOSIDE CHEMISTS. THE RING REMARK 105 OXYGEN ATOM IS LABELLED O4* INSTEAD OF O1*.

REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: NULL

REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS.

REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI REMARK 500 O2P T A 3 NH2 ARG D 14 0.86 REMARK 500 O2P C A 12 OG1 THR C 43 1.31 REMARK 500 O2P T B 3 NH2 ARG C 14 1.38 REMARK 500 NE ARG C 14 OE1 GLN C 21 1.62 REMARK 500 NE ARG D 14 OE1 GLN D 21 1.62 REMARK 500 CZ ARG C 14 OE1 GLN C 21 1.68 REMARK 500 CZ ARG D 14 OE1 GLN D 21 1.68 REMARK 500 O2P A B 2 CB ARG C 20 1.73 REMARK 500 O2P A B 2 CA ARG C 20 1.77 REMARK 500 O1P A A 1 NH2 ARG D 20 1.79 REMARK 500 CD ARG C 40 OE1 GLU C 42 1.85 REMARK 500 CD ARG D 40 OE1 GLU D 42 1.85 REMARK 500 NH2 ARG C 14 OE1 GLN C 21 1.86 REMARK 500 NH2 ARG D 14 OE1 GLN D 21 1.86 REMARK 500 C5M T A 13 CG GLN C 37 1.87 REMARK 500 O2P T A 3 OE1 GLN D 21 1.97 REMARK 500 C5 C A 12 NE2 GLN C 37 2.00 REMARK 500 O2P T A 3 CZ ARG D 14 2.05 REMARK 500 O2P T A 2 CB ARG D 20 2.08 REMARK 500 O2P A B 2 C ARG C 20 2.09 REMARK 500 O2P A B 2 N GLN C 21 2.09 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN C 2 161.77 68.70 REMARK 500 GLN C 4 146.82 62.68 REMARK 500 LYS C 106 -63.63 63.92 REMARK 500 THR C 116 -71.01 79.92 REMARK 500 ASP C 118 -47.97 71.13 REMARK 500 ASP C 122 -63.60 57.78 REMARK 500 MET C 145 144.76 71.55 REMARK 500 ASN C 157 -69.24 72.53 REMARK 500 GLU C 166 -91.74 84.33 REMARK 500 ALA C 171 159.46 62.40 REMARK 500 ASN D 2 161.84 68.62 REMARK 500 GLN D 4 146.77 62.68 REMARK 500 LYS D 106 -63.55 63.90 REMARK 500 THR D 116 -71.73 80.09 REMARK 500 ASP D 118 -46.04 70.68 REMARK 500 ASP D 122 -67.04 57.93 REMARK 500 MET D 145 148.69 69.45 REMARK 500 ASN D 157 -69.28 72.57 REMARK 500 GLU D 166 -79.39 84.76 REMARK 500 ALA D 171 160.35 66.96 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG C 83 GLY C 84 146.81 REMARK 500 ASP C 127 VAL C 128 -148.56 REMARK 500 ASP D 127 VAL D 128 -146.13

DBREF 1QAR C 1 216 UNP P03035 RPC2_BPP22 1 216 DBREF 1QAR D 1 216 UNP P03035 RPC2_BPP22 1 216

SEQRES 1 A 18 A T T T A A G A C T T C T SEQRES 2 A 18 T A A T T SEQRES 1 B 18 A A T T A A G A A G T C T SEQRES 2 B 18 T A A A T SEQRES 1 C 216 MET ASN THR GLN LEU MET GLY GLU ARG ILE ARG ALA ARG SEQRES 2 C 216 ARG LYS LYS LEU LYS ILE ARG GLN ALA ALA LEU GLY LYS SEQRES 3 C 216 MET VAL GLY VAL SER ASN VAL ALA ILE SER GLN TRP GLU SEQRES 4 C 216 ARG SER GLU THR GLU PRO ASN GLY GLU ASN LEU LEU ALA SEQRES 5 C 216 LEU SER LYS ALA LEU GLN CYS SER PRO ASP TYR LEU LEU SEQRES 6 C 216 LYS GLY ASP LEU SER GLN THR ASN VAL ALA TYR HIS SER SEQRES 7 C 216 ARG HIS GLU PRO ARG GLY SER TYR PRO LEU ILE SER TRP SEQRES 8 C 216 VAL SER ALA GLY GLN TRP MET GLU ALA VAL GLU PRO TYR SEQRES 9 C 216 HIS LYS ARG ALA ILE GLU ASN TRP HIS ASP THR THR VAL SEQRES 10 C 216 ASP CYS SER GLU ASP SER PHE TRP LEU ASP VAL GLN GLY SEQRES 11 C 216 ASP SER MET THR ALA PRO ALA GLY LEU SER ILE PRO GLU SEQRES 12 C 216 GLY MET ILE ILE LEU VAL ASP PRO GLU VAL GLU PRO ARG SEQRES 13 C 216 ASN GLY LYS LEU VAL VAL ALA LYS LEU GLU GLY GLU ASN SEQRES 14 C 216 GLU ALA THR PHE LYS LYS LEU VAL MET ASP ALA GLY ARG SEQRES 15 C 216 LYS PHE LEU LYS PRO LEU ASN PRO GLN TYR PRO MET ILE SEQRES 16 C 216 GLU ILE ASN GLY ASN CYS LYS ILE ILE GLY VAL VAL VAL SEQRES 17 C 216 ASP ALA LYS LEU ALA ASN LEU PRO SEQRES 1 D 216 MET ASN THR GLN LEU MET GLY GLU ARG ILE ARG ALA ARG SEQRES 2 D 216 ARG LYS LYS LEU LYS ILE ARG GLN ALA ALA LEU GLY LYS SEQRES 3 D 216 MET VAL GLY VAL SER ASN VAL ALA ILE SER GLN TRP GLU SEQRES 4 D 216 ARG SER GLU THR GLU PRO ASN GLY GLU ASN LEU LEU ALA SEQRES 5 D 216 LEU SER LYS ALA LEU GLN CYS SER PRO ASP TYR LEU LEU SEQRES 6 D 216 LYS GLY ASP LEU SER GLN THR ASN VAL ALA TYR HIS SER SEQRES 7 D 216 ARG HIS GLU PRO ARG GLY SER TYR PRO LEU ILE SER TRP SEQRES 8 D 216 VAL SER ALA GLY GLN TRP MET GLU ALA VAL GLU PRO TYR SEQRES 9 D 216 HIS LYS ARG ALA ILE GLU ASN TRP HIS ASP THR THR VAL SEQRES 10 D 216 ASP CYS SER GLU ASP SER PHE TRP LEU ASP VAL GLN GLY SEQRES 11 D 216 ASP SER MET THR ALA PRO ALA GLY LEU SER ILE PRO GLU SEQRES 12 D 216 GLY MET ILE ILE LEU VAL ASP PRO GLU VAL GLU PRO ARG SEQRES 13 D 216 ASN GLY LYS LEU VAL VAL ALA LYS LEU GLU GLY GLU ASN SEQRES 14 D 216 GLU ALA THR PHE LYS LYS LEU VAL MET ASP ALA GLY ARG SEQRES 15 D 216 LYS PHE LEU LYS PRO LEU ASN PRO GLN TYR PRO MET ILE SEQRES 16 D 216 GLU ILE ASN GLY ASN CYS LYS ILE ILE GLY VAL VAL VAL SEQRES 17 D 216 ASP ALA LYS LEU ALA ASN LEU PRO

HELIX 1 1 LEU C 5 LYS C 18 1 14 HELIX 2 2 ARG C 20 GLY C 29 1 10 HELIX 3 3 SER C 31 ARG C 40 1 10 HELIX 4 4 ASN C 46 LEU C 57 1 12 HELIX 5 5 SER C 60 LYS C 66 1 7 HELIX 6 6 GLU C 81 SER C 85 5 5 HELIX 7 7 GLN C 96 VAL C 101 1 6 HELIX 8 8 ARG C 107 ASP C 114 1 8 HELIX 9 9 LEU D 5 LYS D 18 1 14 HELIX 10 10 ARG D 20 GLY D 29 1 10 HELIX 11 11 SER D 31 ARG D 40 1 10 HELIX 12 12 ASN D 46 LEU D 57 1 12 HELIX 13 13 SER D 60 LYS D 66 1 7 HELIX 14 14 GLN D 96 VAL D 101 1 6 HELIX 15 15 ARG D 107 ASP D 114 1 8

SHEET 1 A 2 LEU C 160 VAL C 161 0 SHEET 2 A 2 ILE C 195 GLU C 196 -1 O ILE C 195 N VAL C 161 SHEET 1 B 2 LYS C 174 LEU C 176 0 SHEET 2 B 2 ARG C 182 PHE C 184 -1 N LYS C 183 O LYS C 175 SHEET 1 C 2 LEU D 160 VAL D 161 0 SHEET 2 C 2 ILE D 195 GLU D 196 -1 O ILE D 195 N VAL D 161 SHEET 1 D 2 LYS D 174 LEU D 176 0 SHEET 2 D 2 ARG D 182 PHE D 184 -1 N LYS D 183 O LYS D 175

CISPEP 1 LYS C 186 PRO C 187 0 1.16 CISPEP 2 TYR C 192 PRO C 193 0 3.55 CISPEP 3 LYS D 186 PRO D 187 0 2.94 CISPEP 4 TYR D 192 PRO D 193 0 3.68

CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1

ORIGX1 1.000000 0.000000 0.000000 0.00000

ORIGX2 0.000000 1.000000 0.000000 0.00000

ORIGX3 0.000000 0.000000 1.000000 0.00000

SCALE1 1.000000 0.000000 0.000000 0.00000

SCALE2 0.000000 1.000000 0.000000 0.00000

SCALE3 0.000000 0.000000 1.000000 0.00000