1GFX - Header Asymmetric Unit

HEADER TRANSCRIPTION/DNA 22-JUN-00 1GFX

TITLE UMUD' BASED MODEL OF A LAMBDA REPRESSOR TETRAMER (TWO TITLE 2 DIMERS) BOUND TO TWO ADJACENT OPERATOR SITES

CAVEAT 1GFX INCORRECT CHIRAL CARBON CENTER(S)

COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (BACTERIOPHAGE LAMBDA REPRESSOR CI); COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: RESIDUES 1-236; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (44-MER); COMPND 7 CHAIN: E; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (44-MER); COMPND 11 CHAIN: F; COMPND 12 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTERIOPHAGE LAMBDA; SOURCE 3 ORGANISM_COMMON: BACTERIOPHAGE; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 MOL_ID: 3; SOURCE 7 SYNTHETIC: YES

KEYWDS FULL LAMBDA REPRESSOR, GENE REGULATION, OPERATOR SITES

EXPDTA THEORETICAL MODEL

AUTHOR R.CHATTOPADHYAYA,K.GHOSH

REVDAT 5 21-JUN-05 1GFX 1 JRNL REVDAT 4 11-MAY-04 1GFX 1 REMARK REVDAT 3 10-FEB-04 1GFX 1 REMARK REVDAT 2 22-MAR-02 1GFX 1 REMARK REVDAT 1 03-JUL-00 1GFX 0

JRNL AUTH R.CHATTOPADHYAYA,K.GHOSH JRNL TITL A COMPARATIVE THREE-DIMENSIONAL MODEL OF THE JRNL TITL 2 CARBOXY-TERMINAL DOMAIN OF THE LAMBDA REPRESSOR JRNL TITL 3 AND ITS USE TO BUILD INTACT REPRESSOR TETRAMER JRNL TITL 4 MODELS BOUND TO ADJACENT OPERATOR SITES JRNL REF J.STRUCT.BIOL. V. 141 103 2003 JRNL REFN ASTM JSBIEM US ISSN 1047-8477

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.J.BEAMER,C.O.PABO REMARK 1 TITL REFINED 1.8 A CRYSTAL STRUCTURE OF THE LAMBDA REMARK 1 TITL 2 REPRESSOR-OPERATOR COMPLEX REMARK 1 REF J.MOL.BIOL. V. 227 177 1992 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH C.O.PABO,M.LEWIS REMARK 1 TITL THE OPERATOR-BINDING DOMAIN OF LAMBDA REPRESSOR: REMARK 1 TITL 2 STRUCTURE AND DNA RECOGNITION REMARK 1 REF NATURE V. 298 443 1982 REMARK 1 REFN ASTM NATUAS UK ISSN 0028-0836 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 UNDERSTANDING REMARK 1 TITL 2 PROTEIN-DNA INTERACTIONS AND PROTEIN STABILITY REMARK 1 REF ADV.PROT.CHEM. V. 40 1 1990 REMARK 1 REFN 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 A.D.JOHNSON,A.R.POTEETE,G.LAUER,R.T.SAUER, REMARK 1 AUTH 2 G.K.ACKERS,M.PTASHNE REMARK 1 TITL LAMBDA REPRESSOR AND CRO COMPONENTS OF AN REMARK 1 TITL 2 EFFICIENT MOLECULAR SWITCH REMARK 1 REF NATURE V. 294 217 1981 REMARK 1 REFN ASTM NATUAS UK ISSN 0028-0836 REMARK 1 REFERENCE 7 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 AND DEVELOPMENT V. 8 1212 1994 REMARK 1 REFN US ISSN 0890-9369 REMARK 1 REFERENCE 8 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 9 REMARK 1 AUTH D.S.BURZ,G.K.ACKERS REMARK 1 TITL SELF-ASSEMBLY OF BACTERIOPHAGE LAMBDA CI REMARK 1 TITL 2 REPRESSOR: EFFECTS OF SINGLE-SITE MUTATIONS ON THE REMARK 1 TITL 3 MONOMER-DIMER EQUILIBRIUM REMARK 1 REF BIOCHEMISTRY V. 33 8399 1994 REMARK 1 REFN ASTM BICHAW US ISSN 0006-2960 REMARK 1 REFERENCE 10 REMARK 1 AUTH D.S.BURZ,G.K.ACKERS REMARK 1 TITL SINGLE-SITE MUTATIONS IN THE C-TERMINAL DOMAIN OF REMARK 1 TITL 2 BACTERIOPHAGE LAMBDA CI REPRESSOR ALTER REMARK 1 TITL 3 COOPERATIVE INTERACTIONS BETWEEN DIMERS ADJACENTLY REMARK 1 TITL 4 BOUND TO OR REMARK 1 REF BIOCHEMISTRY V. 33 8406 1994 REMARK 1 REFN ASTM BICHAW US ISSN 0006-2960 REMARK 1 REFERENCE 11 REMARK 1 AUTH K.S.KOBLAN,G.K.ACKERS REMARK 1 TITL ENERGETICS OF SUBUNIT DIMERIZATION IN REMARK 1 TITL 2 BACTERIOPHAGE LAMBDA CI REPRESSOR: LINKAGE TO REMARK 1 TITL 3 PROTONS, TEMPERATURE, AND KCL REMARK 1 REF BIOCHEMISTRY V. 30 7817 1991 REMARK 1 REFN ASTM BICHAW US ISSN 0006-2960 REMARK 1 REFERENCE 12 REMARK 1 AUTH K.S.KOBLAN,G.K.ACKERS REMARK 1 TITL COOPERATIVE PROTEIN-DNA INTERACTIONS: EFFECTS OF REMARK 1 TITL 2 KCL ON LAMBDA CI BINDING TO OR REMARK 1 REF BIOCHEMISTRY V. 30 7822 1991 REMARK 1 REFN ASTM BICHAW US ISSN 0006-2960 REMARK 1 REFERENCE 13 REMARK 1 AUTH D.STRAHS,M.BRENOWITZ REMARK 1 TITL DNA CONFORMATIONAL CHANGES ASSOCIATED WITH THE REMARK 1 TITL 2 COOPERATIVE BINDING OF CI-REPRESSOR OF REMARK 1 TITL 3 BACTERIOPHAGE LAMBDA TO OR REMARK 1 REF J.MOL.BIOL. V. 244 494 1994 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REFERENCE 14 REMARK 1 AUTH J.W.LITTLE REMARK 1 TITL AUTODIGESTION OF LEXA AND PHAGE LAMBDA REPRESSOR REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 81 1375 1984 REMARK 1 REFN ASTM PNASA6 US ISSN 0027-8424 REMARK 1 REFERENCE 15 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 16 REMARK 1 AUTH G.GHOSH,G.VAN DUYNE,S.GHOSH,P.B.SIGLER REMARK 1 TITL STRUCTURE OF NF-KAPPA B P50 HOMODIMER BOUND TO A REMARK 1 TITL 2 KAPPA B SITE REMARK 1 REF NATURE V. 373 303 1995 REMARK 1 REFN ASTM NATUAS UK ISSN 0028-0836 REMARK 1 REFERENCE 17 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 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 1 REFERENCE 19 REMARK 1 AUTH R.CHATTOPADHYAYA,K.GHOSH REMARK 1 TITL A COMPARATIVE THREE-DIMENSIONAL MODEL OF THE REMARK 1 TITL 2 CARBOXY-TERMINAL DOMAIN OF THE LAMBDA REPRESSOR REMARK 1 TITL 3 AND ITS USE TO BUILD INTACT REPRESSOR TETRAMER REMARK 1 TITL 4 MODELS BOUND TO ADJACENT OPERATOR SITES. REMARK 1 REF J.STRUCT.BIOL. V. 141 103 2003 REMARK 1 REFN ASTM JSBIEM US ISSN 1047-8477

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 1GFX COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998

REMARK 7 REMARK 7 THE BACTERIOPHAGE LAMBDA CI REPRESSOR IS A TWO DOMAIN, REMARK 7 236 RESIDUE REGULATORY PROTEIN. THE N-DOMAIN (1-92) REMARK 7 BINDS DNA, WHILE THE C-DOMAIN (93-236) IS INVOLVED IN REMARK 7 PROTEIN-PROTEIN CONTACTS. THE CI REPRESSOR BINDS TWO REMARK 7 SETS OF THREE HOMOLOGOUS, PARTIALLY SYMMETRIC BINDING REMARK 7 SITES (OR1,OR2,OR3,OL1,OL2,OL3) KNOWN AS OPERATOR REMARK 7 SITES. AT EACH OPERATOR SITE, A DIMER OF THE REPRESSOR REMARK 7 BINDS (REF.6 ABOVE). REMARK 7 REMARK 7 THE CRYSTAL STRUCTURES OF THE N-DOMAIN (1-92; REF. 2 REMARK 7 ABOVE; PDB CODE 1LRP) AND THE N-DOMAIN COMPLEXED WITH REMARK 7 THE OL1 OPERATOR SITE (REF.1 ABOVE; PDB CODE 1LMB) ARE REMARK 7 AVAILABLE. HOWEVER, THE INTACT CI REPRESSOR OR ITS REMARK 7 C-DOMAIN (IT IS POSSIBLE TO PURIFY A NUMBER OF REMARK 7 C-TERMINAL FRAGMENTS SUCH AS 93-236, 112-236, 132-236) REMARK 7 COULD NOT YET BE STUDIED BY X-RAY CRYSTALLOGRAPHY. REMARK 7 REMARK 7 COMPARATIVE MODEL REMARK 7 REMARK 7 OUR AB INITIO MODEL OF THE LAMBDA CI REPRESSOR WAS REMARK 7 PREVIOUSLY DEPOSITED IN THE PDB IN MARCH 1999 (1LMD). REMARK 7 HOWEVER, BOTH A SCOP DATABASE SEARCH AND THE FOLD REMARK 7 RECOGNITION SEARCH OF FISCHER AND EISENBERG INDICATED REMARK 7 THE UMUD' STRUCTURE AS THE MOST PROBABLE TEMPLATE. REMARK 7 IN OUR AB INITIO MODEL (1LMD) WE HAD RULED OUT UMUD' REMARK 7 AS A POSSIBLE FOLD SINCE ACCORDING TO THE ALIGNMENT REMARK 7 PRESENTED IN REF. (18) ABOVE, BOTH CYS 215 AND CYS REMARK 7 219 WOULD BE EXPOSED TO THE SOLVENT; HENCE THEIR SIDE REMARK 7 CHAINS THIOLS SHOULD HAVE BEEN REACTIVE TO DTNB REMARK 7 CONTRARY TO EXPERIMENTAL RESULTS (REF. 5 ABOVE). REMARK 7 REMARK 7 WE HAVE USED THE UMUD' CRYSTAL STRUCTURE, BUT A REMARK 7 SLIGHTLY DIFFERENT ALIGNMENT COMPARED TO THE ONE REMARK 7 PRESENTED IN REF. (18). IN OUR ALIGNMENT, BOTH CYS REMARK 7 SIDE CHAIN SULFUR ATOMS ARE BURIED IN THE DOMAIN, THUS REMARK 7 EXPLAINING THE INERTNESS OF THE CYS 215 AND 219 SIDE REMARK 7 CHAINS, THOUGH THE THIOL HYDROGEN ATOMS ARE EXPOSED. REMARK 7 DTNB CANNOT REACT SINCE THE NUCLEOPHILIC ATTACK REMARK 7 FROM THE THIOL SULFUR ATOMS IS PREVENTED. REMARK 7 REMARK 7 WE HAVE USED THE PDB ENTRY 1LMB TO MODEL THE OPERATOR REMARK 7 SITES AND THE ATTACHED N-DOMAINS. HENCE RESIDUES 1-92 REMARK 7 IN OUR MODEL POSSESS AN IDENTICAL STRUCTURE TO THIS REMARK 7 CRYSTAL STRUCTURE. OUR MODEL CONTAINS TWO SUCH DIMERS REMARK 7 WITH SOME INTERVENING BASE PAIRS CORRESPONDING TO THE REMARK 7 REGION BETWEEN OR1 AND OR2 SITES. REMARK 7 REMARK 7 CIRCULAR DICHROISM SPECTRA FOR THE VARIOUS PURIFIED REMARK 7 C-TERMINAL FRAGMENTS WERE RECORDED AND THEY TALLIED REMARK 7 WITH OUR SECONDARY STRUCTURE PREDICTIONS FOR THE REMARK 7 C-DOMAIN. AMOUNT OF HELIX CONTENT DECREASED AS THE REMARK 7 SIZE OF THE C-TERMINAL FRAGMENT DECREASED, WITH REMARK 7 THE FRAGMENT 132-236 SHOWING ALMOST PURE BETA REMARK 7 SHEET CD SPECTRUM. A TOTAL OF EIGHT BETA STRANDS REMARK 7 ARE PREDICTED IN THE REGION 93-236 BY OUR METHOD. REMARK 7 THESE ARE DESIGNATED AS BETA1 THROUGH BETA8. REMARK 7 REMARK 7 FTIR DATA IN OUR LAB SHOWS PRESENCE OF HELICAL REMARK 7 CONTENT IN THE 93-236 FRAGMENT, BUT NOT IN THE REMARK 7 132-236 FRAGMENT, CONSISTENT WITH BOTH SECONDARY REMARK 7 STRUCTURE PREDICTION AND CIRCULAR DICHROISM DATA. REMARK 7 REMARK 7 THE CATALYTIC SER 149 AND LYS 192, WHOSE SIDE REMARK 7 CHAINS ARE CLOSE TO EACH OTHER IN THE UMUD' REMARK 7 BASED C-DOMAIN, MUST ALSO BE CLOSE TO THE REMARK 7 SUBSTRATE OF IN VITRO AUTOCLEAVAGE, ALA 111 - REMARK 7 GLY 112. THIS IS SUGGESTED BY THE REMARK 7 LARGE VALUE OF THE ACTIVATION ENERGY FOR THE REMARK 7 IN VITRO AUTOCLEAVAGE OF LAMBDA REPRESSOR OF 21.6 REMARK 7 KCAL / MOLE MEASURED BY US. THE PREEXPONENTIAL REMARK 7 ARRHENIUS FACTOR IS ABOUT 2 BILLION TO 20 BILLION REMARK 7 PER SECOND, INDICATING THE NUMBER OF PROPERLY REMARK 7 ORIENTED COLLISIONS. SUCH A HIGH NUMBER OF COLLISIONS REMARK 7 REQUIRE THAT THE CLEAVAGE SITE BE CLOSE TO THE REMARK 7 CATALYTIC SITE. REMARK 7 REMARK 7 LIKE OUR LEXA MODEL(1QAA), WE PROPOSE THAT NORMALLY REMARK 7 AUTOCLEAVAGE DOES NOT OCCUR AS THE ALA 111 - REMARK 7 GLY 112 IS NOT CLOSE ENOUGH TO THE CATALYTIC REMARK 7 GROUPS. BOTH SER 149 OG ATOM AND THE LYS 192 NZ REMARK 7 ARE ABOUT 8-9 ANGSTROMS AWAY REMARK 7 FROM THE ALA 111 C ATOM. AT ELEVATED PH, OR UNDER REMARK 7 THE ACTIVATION OF RECA, A STRUCTURAL REARRANGEMENT REMARK 7 OCCURS BRINGING THE CATALYTIC GROUPS CLOSER TO REMARK 7 ALA 111 C. REMARK 7 REMARK 7 THE VARIOUS MUTAGENESIS STUDIES (REFS.4,7,9,10 AND REMARK 7 MANY MORE) HELPED US TO BRING SPECIFIC RESIDUES OF REMARK 7 LAMBDA REPRESSOR ON THE EXTERIOR SURFACE, THUS REMARK 7 PROVIDING ADDITIONAL CHECKS FOR OUR MODEL. REMARK 7 IN OUR MODELS, THE REGION 195-210 CONTAINING BETA6 REMARK 7 AND TWO ADJACENT LOOPS ARE MOST CRUCIAL FOR THE REMARK 7 COOPERATIVE OR DIMER-DIMER INTERACTIONS. IT WILL BE REMARK 7 EXPLAINED IN OUR PUBLICATIONS HOW AND WHY THIS REMARK 7 MODEL IS LARGELY CONSISTENT WITH ACCUMULATED REMARK 7 BIOCHEMICAL AND BIOPHYSICAL DATA ABOUT THE LAMBDA REMARK 7 REPRESSOR. REMARK 7 REMARK 7 1 44 REMARK 7 5'-TATATCACCGCCAGTGGTATTTATGATATCACCGCCAGTGGTAT-3' REMARK 7 3'-TATAGTGGCGGTCACCATAAATACTATAGTGGCGGTCACCATAA-5' REMARK 7 88 45 REMARK 7 REMARK 7 THE CRYSTAL STRUCTURE 1LMB SHOWS A BEND OF ABOUT 16 REMARK 7 DEGREES IN THE HELIX AXIS IN OL1. SINCE WE HAVE TWO REMARK 7 OF THEM, ABOUT 30 DEGREES OF BENDING ARE DUE TO THE REMARK 7 TWO OL1 SITES IN THE ABOVE DNA MOLECULE. THE INTER REMARK 7 -VENING BASE PAIRS EXHIBIT AN AVERAGE TWIST OF 23-27 REMARK 7 DEGREES. WATSON-CRICK BASE PAIRING IS PRESENT, REMARK 7 THOUGH DISTORTED IN SOME INTERVENING BASE PAIRS (21- REMARK 7 25) RISE PER STEP IS HIGHER THAN NORMAL AND AN REMARK 7 ADDITIONAL BEND OF 15 DEGREES IS SEEN. REMARK 7 REMARK 7 ATOMS ORIGINALLY TAKEN FROM 1LMB BEAR THEIR ORIGINAL REMARK 7 TEMPERATURE FACTORS AND CAN BE IDENTIFIED AS SUCH.

REMARK 8 REMARK 8 MODEL BUILDING FOR THE COMPLETE LAMBDA REPRESSOR REMARK 8 TETRAMER AND ASSOCIATED OPERATOR DNA WAS CARRIED OUT REMARK 8 USING THE INSIGHT-II PACKAGE INCLUDING PROGRAMS REMARK 8 DISCOVER AND HOMOLOGY

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JUN-2000. REMARK 100 THE RCSB ID CODE IS RCSB001477.

REMARK 103 REMARK 103 THERE ARE NON-WATSON-CRICK HYDROGEN BONDS BETWEEN THE REMARK 103 FOLLOWING ATOMS: REMARK 103 N1 A E 4 AND N3 T F 86 REMARK 103 N2 G E 17 AND O2 C F 73 REMARK 103 N3 T E 18 AND N1 A F 72 REMARK 103 N1 A E 26 AND N3 T F 64 REMARK 103 N3 T E 27 AND N1 A F 63 REMARK 103 N1 A E 28 AND N3 T F 62 REMARK 103 N3 T E 39 AND N1 A F 51 REMARK 103 N3 T E 42 AND N1 A F 48

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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER B 1 REMARK 465 THR B 2 REMARK 465 LYS B 3 REMARK 465 LYS B 4 REMARK 465 LYS B 5 REMARK 465 SER D 1 REMARK 465 THR D 2 REMARK 465 LYS D 3 REMARK 465 LYS D 4 REMARK 465 LYS D 5

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 O1P T E 27 OH TYR C 22 1.60 REMARK 500 O1P G E 38 ND2 ASN D 61 1.72 REMARK 500 O2P T F 83 N GLY A 43 1.79 REMARK 500 O2P T F 71 N GLN B 33 1.88 REMARK 500 O2P T E 27 OH TYR C 22 1.89 REMARK 500 O2P T E 27 N GLN C 33 1.93 REMARK 500 O2P A E 37 N ALA D 56 2.02 REMARK 500 O1P T F 71 OH TYR B 22 2.05 REMARK 500 P T E 27 OH TYR C 22 2.08 REMARK 500 O2P T E 39 CB MET D 42 2.09 REMARK 500 O6 G E 40 OG SER D 45 2.15 REMARK 500 O1P G F 81 ND2 ASN A 58 2.16 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 THR C 154 CA - CB - CG2 ANGL. DEV. = 20.5 DEGREES REMARK 500 PRO C 211 CB - CA - C ANGL. DEV. = 22.3 DEGREES REMARK 500 PRO C 211 N - CA - CB ANGL. DEV. =-30.9 DEGREES 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 SER A 96 -50.65 78.19 REMARK 500 THR A 133 -86.73 61.72 REMARK 500 LYS A 134 -74.59 68.33 REMARK 500 ASP A 138 -45.03 71.13 REMARK 500 SER A 156 -83.15 67.14 REMARK 500 SER A 198 145.22 69.43 REMARK 500 GLN A 200 -83.05 66.12 REMARK 500 THR B 133 -86.71 61.71 REMARK 500 LYS B 134 -74.53 68.28 REMARK 500 ASP B 138 -45.10 71.11 REMARK 500 SER B 156 -83.13 67.15 REMARK 500 SER B 198 145.21 69.40 REMARK 500 GLN B 200 -82.99 66.02 REMARK 500 THR C 133 -86.68 61.73 REMARK 500 LYS C 134 -74.69 68.36 REMARK 500 ASP C 138 -45.08 71.06 REMARK 500 SER C 156 -83.12 67.05 REMARK 500 SER C 198 145.19 69.41 REMARK 500 GLN C 200 -83.13 66.19 REMARK 500 THR D 133 -86.61 61.71 REMARK 500 LYS D 134 -74.51 68.20 REMARK 500 ASP D 138 -45.06 71.06 REMARK 500 SER D 156 -83.30 67.30 REMARK 500 SER D 198 145.23 69.42 REMARK 500 GLN D 200 -83.01 65.98 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 PRO C 208 GLN C 209 142.88

REMARK 999 REMARK 999 THERE ARE FOUR LAMBDA REPRESSOR MOLECULES WITH CHAIN REMARK 999 IDENTIFIERS *A*,*B*,*C* AND *D* RESPECTIVELY. OPERATOR REMARK 999 DNA CHAIN IDENTIFIERS CONTAIN NUCLEOTIDE TYPE AND REMARK 999 SEQUENCE NUMBER FROM THE 5 PRIME END, NUMBER VARYING REMARK 999 FROM 1-44 AND 45-88 FOR THE TWO STRANDS. WATSON-CRICK REMARK 999 BASE PAIRING OCCURS BETWEEN 2-44 AND 46-88.

DBREF 1GFX A 1 236 UNP P03034 RPC1_LAMBD 1 236 DBREF 1GFX B 1 236 UNP P03034 RPC1_LAMBD 1 236 DBREF 1GFX C 1 236 UNP P03034 RPC1_LAMBD 1 236 DBREF 1GFX D 1 236 UNP P03034 RPC1_LAMBD 1 236

SEQRES 1 A 236 SER THR LYS LYS LYS PRO LEU THR GLN GLU GLN LEU GLU SEQRES 2 A 236 ASP ALA ARG ARG LEU LYS ALA ILE TYR GLU LYS LYS LYS SEQRES 3 A 236 ASN GLU LEU GLY LEU SER GLN GLU SER VAL ALA ASP LYS SEQRES 4 A 236 MET GLY MET GLY GLN SER GLY VAL GLY ALA LEU PHE ASN SEQRES 5 A 236 GLY ILE ASN ALA LEU ASN ALA TYR ASN ALA ALA LEU LEU SEQRES 6 A 236 ALA LYS ILE LEU LYS VAL SER VAL GLU GLU PHE SER PRO SEQRES 7 A 236 SER ILE ALA ARG GLU ILE TYR GLU MET TYR GLU ALA VAL SEQRES 8 A 236 SER MET GLN PRO SER LEU ARG SER GLU TYR GLU TYR PRO SEQRES 9 A 236 VAL PHE SER HIS VAL GLN ALA GLY MET PHE SER PRO GLU SEQRES 10 A 236 LEU ARG THR PHE THR LYS GLY ASP ALA GLU ARG TRP VAL SEQRES 11 A 236 SER THR THR LYS LYS ALA SER ASP SER ALA PHE TRP LEU SEQRES 12 A 236 GLU VAL GLU GLY ASN SER MET THR ALA PRO THR GLY SER SEQRES 13 A 236 LYS PRO SER PHE PRO ASP GLY MET LEU ILE LEU VAL ASP SEQRES 14 A 236 PRO GLU GLN ALA VAL GLU PRO GLY ASP PHE CYS ILE ALA SEQRES 15 A 236 ARG LEU GLY GLY ASP GLU PHE THR PHE LYS LYS LEU ILE SEQRES 16 A 236 ARG ASP SER GLY GLN VAL PHE LEU GLN PRO LEU ASN PRO SEQRES 17 A 236 GLN TYR PRO MET ILE PRO CYS ASN GLU SER CYS SER VAL SEQRES 18 A 236 VAL GLY LYS VAL ILE ALA SER GLN TRP PRO GLU GLU THR SEQRES 19 A 236 PHE GLY SEQRES 1 B 236 SER THR LYS LYS LYS PRO LEU THR GLN GLU GLN LEU GLU SEQRES 2 B 236 ASP ALA ARG ARG LEU LYS ALA ILE TYR GLU LYS LYS LYS SEQRES 3 B 236 ASN GLU LEU GLY LEU SER GLN GLU SER VAL ALA ASP LYS SEQRES 4 B 236 MET GLY MET GLY GLN SER GLY VAL GLY ALA LEU PHE ASN SEQRES 5 B 236 GLY ILE ASN ALA LEU ASN ALA TYR ASN ALA ALA LEU LEU SEQRES 6 B 236 ALA LYS ILE LEU LYS VAL SER VAL GLU GLU PHE SER PRO SEQRES 7 B 236 SER ILE ALA ARG GLU ILE TYR GLU MET TYR GLU ALA VAL SEQRES 8 B 236 SER MET GLN PRO SER LEU ARG SER GLU TYR GLU TYR PRO SEQRES 9 B 236 VAL PHE SER HIS VAL GLN ALA GLY MET PHE SER PRO GLU SEQRES 10 B 236 LEU ARG THR PHE THR LYS GLY ASP ALA GLU ARG TRP VAL SEQRES 11 B 236 SER THR THR LYS LYS ALA SER ASP SER ALA PHE TRP LEU SEQRES 12 B 236 GLU VAL GLU GLY ASN SER MET THR ALA PRO THR GLY SER SEQRES 13 B 236 LYS PRO SER PHE PRO ASP GLY MET LEU ILE LEU VAL ASP SEQRES 14 B 236 PRO GLU GLN ALA VAL GLU PRO GLY ASP PHE CYS ILE ALA SEQRES 15 B 236 ARG LEU GLY GLY ASP GLU PHE THR PHE LYS LYS LEU ILE SEQRES 16 B 236 ARG ASP SER GLY GLN VAL PHE LEU GLN PRO LEU ASN PRO SEQRES 17 B 236 GLN TYR PRO MET ILE PRO CYS ASN GLU SER CYS SER VAL SEQRES 18 B 236 VAL GLY LYS VAL ILE ALA SER GLN TRP PRO GLU GLU THR SEQRES 19 B 236 PHE GLY SEQRES 1 C 236 SER THR LYS LYS LYS PRO LEU THR GLN GLU GLN LEU GLU SEQRES 2 C 236 ASP ALA ARG ARG LEU LYS ALA ILE TYR GLU LYS LYS LYS SEQRES 3 C 236 ASN GLU LEU GLY LEU SER GLN GLU SER VAL ALA ASP LYS SEQRES 4 C 236 MET GLY MET GLY GLN SER GLY VAL GLY ALA LEU PHE ASN SEQRES 5 C 236 GLY ILE ASN ALA LEU ASN ALA TYR ASN ALA ALA LEU LEU SEQRES 6 C 236 ALA LYS ILE LEU LYS VAL SER VAL GLU GLU PHE SER PRO SEQRES 7 C 236 SER ILE ALA ARG GLU ILE TYR GLU MET TYR GLU ALA VAL SEQRES 8 C 236 SER MET GLN PRO SER LEU ARG SER GLU TYR GLU TYR PRO SEQRES 9 C 236 VAL PHE SER HIS VAL GLN ALA GLY MET PHE SER PRO GLU SEQRES 10 C 236 LEU ARG THR PHE THR LYS GLY ASP ALA GLU ARG TRP VAL SEQRES 11 C 236 SER THR THR LYS LYS ALA SER ASP SER ALA PHE TRP LEU SEQRES 12 C 236 GLU VAL GLU GLY ASN SER MET THR ALA PRO THR GLY SER SEQRES 13 C 236 LYS PRO SER PHE PRO ASP GLY MET LEU ILE LEU VAL ASP SEQRES 14 C 236 PRO GLU GLN ALA VAL GLU PRO GLY ASP PHE CYS ILE ALA SEQRES 15 C 236 ARG LEU GLY GLY ASP GLU PHE THR PHE LYS LYS LEU ILE SEQRES 16 C 236 ARG ASP SER GLY GLN VAL PHE LEU GLN PRO LEU ASN PRO SEQRES 17 C 236 GLN TYR PRO MET ILE PRO CYS ASN GLU SER CYS SER VAL SEQRES 18 C 236 VAL GLY LYS VAL ILE ALA SER GLN TRP PRO GLU GLU THR SEQRES 19 C 236 PHE GLY SEQRES 1 D 236 SER THR LYS LYS LYS PRO LEU THR GLN GLU GLN LEU GLU SEQRES 2 D 236 ASP ALA ARG ARG LEU LYS ALA ILE TYR GLU LYS LYS LYS SEQRES 3 D 236 ASN GLU LEU GLY LEU SER GLN GLU SER VAL ALA ASP LYS SEQRES 4 D 236 MET GLY MET GLY GLN SER GLY VAL GLY ALA LEU PHE ASN SEQRES 5 D 236 GLY ILE ASN ALA LEU ASN ALA TYR ASN ALA ALA LEU LEU SEQRES 6 D 236 ALA LYS ILE LEU LYS VAL SER VAL GLU GLU PHE SER PRO SEQRES 7 D 236 SER ILE ALA ARG GLU ILE TYR GLU MET TYR GLU ALA VAL SEQRES 8 D 236 SER MET GLN PRO SER LEU ARG SER GLU TYR GLU TYR PRO SEQRES 9 D 236 VAL PHE SER HIS VAL GLN ALA GLY MET PHE SER PRO GLU SEQRES 10 D 236 LEU ARG THR PHE THR LYS GLY ASP ALA GLU ARG TRP VAL SEQRES 11 D 236 SER THR THR LYS LYS ALA SER ASP SER ALA PHE TRP LEU SEQRES 12 D 236 GLU VAL GLU GLY ASN SER MET THR ALA PRO THR GLY SER SEQRES 13 D 236 LYS PRO SER PHE PRO ASP GLY MET LEU ILE LEU VAL ASP SEQRES 14 D 236 PRO GLU GLN ALA VAL GLU PRO GLY ASP PHE CYS ILE ALA SEQRES 15 D 236 ARG LEU GLY GLY ASP GLU PHE THR PHE LYS LYS LEU ILE SEQRES 16 D 236 ARG ASP SER GLY GLN VAL PHE LEU GLN PRO LEU ASN PRO SEQRES 17 D 236 GLN TYR PRO MET ILE PRO CYS ASN GLU SER CYS SER VAL SEQRES 18 D 236 VAL GLY LYS VAL ILE ALA SER GLN TRP PRO GLU GLU THR SEQRES 19 D 236 PHE GLY SEQRES 1 E 44 T A T A T C A C C G C C A SEQRES 2 E 44 G T G G T A T T T A T G A SEQRES 3 E 44 T A T C A C C G C C A G T SEQRES 4 E 44 G G T A T SEQRES 1 F 44 A A T A C C A C T G G C G SEQRES 2 F 44 G T G A T A T C A T A A A SEQRES 3 F 44 T A C C A C T G G C G G T SEQRES 4 F 44 G A T A T

HELIX 1 1 THR A 8 GLY A 30 1 23 HELIX 2 2 SER A 32 GLY A 41 1 10 HELIX 3 3 GLY A 43 ASN A 52 1 10 HELIX 4 4 ASN A 58 LYS A 70 1 13 HELIX 5 5 SER A 72 PHE A 76 5 5 HELIX 6 6 SER A 77 MET A 93 1 17 HELIX 7 7 PHE A 114 ARG A 119 1 6 HELIX 8 8 ASP A 125 THR A 132 1 8 HELIX 9 9 THR B 8 GLY B 30 1 23 HELIX 10 10 SER B 32 MET B 40 1 9 HELIX 11 11 GLY B 43 ASN B 52 1 10 HELIX 12 12 ASN B 58 LYS B 70 1 13 HELIX 13 13 SER B 72 PHE B 76 5 5 HELIX 14 14 SER B 77 MET B 93 1 17 HELIX 15 15 PHE B 114 ARG B 119 1 6 HELIX 16 16 ASP B 125 THR B 132 1 8 HELIX 17 17 THR C 8 GLY C 30 1 23 HELIX 18 18 SER C 32 GLY C 41 1 10 HELIX 19 19 GLY C 43 ASN C 52 1 10 HELIX 20 20 ASN C 58 LYS C 70 1 13 HELIX 21 21 SER C 72 PHE C 76 5 5 HELIX 22 22 SER C 77 MET C 93 1 17 HELIX 23 23 PHE C 114 ARG C 119 1 6 HELIX 24 24 ASP C 125 THR C 132 1 8 HELIX 25 25 THR D 8 GLY D 30 1 23 HELIX 26 26 SER D 32 MET D 40 1 9 HELIX 27 27 GLY D 43 ASN D 52 1 10 HELIX 28 28 ASN D 58 LYS D 70 1 13 HELIX 29 29 SER D 72 PHE D 76 5 5 HELIX 30 30 SER D 77 MET D 93 1 17 HELIX 31 31 PHE D 114 ARG D 119 1 6 HELIX 32 32 ASP D 125 THR D 132 1 8

SHEET 1 A 7 PHE A 141 GLU A 144 0 SHEET 2 A 7 LEU A 165 ASP A 169 -1 N ILE A 166 O LEU A 143 SHEET 3 A 7 CYS A 219 GLN A 229 -1 O LYS A 224 N ASP A 169 SHEET 4 A 7 PHE A 179 LEU A 184 -1 O PHE A 179 N VAL A 225 SHEET 5 A 7 PHE A 189 ILE A 195 -1 O THR A 190 N ALA A 182 SHEET 6 A 7 PHE A 202 GLN A 204 -1 O PHE A 202 N ILE A 195 SHEET 7 A 7 ILE A 213 PRO A 214 -1 O ILE A 213 N LEU A 203 SHEET 1 B 7 PHE B 141 GLU B 144 0 SHEET 2 B 7 LEU B 165 ASP B 169 -1 N ILE B 166 O LEU B 143 SHEET 3 B 7 CYS B 219 GLN B 229 -1 O LYS B 224 N ASP B 169 SHEET 4 B 7 PHE B 179 LEU B 184 -1 O PHE B 179 N VAL B 225 SHEET 5 B 7 PHE B 189 ILE B 195 -1 O THR B 190 N ALA B 182 SHEET 6 B 7 PHE B 202 GLN B 204 -1 O PHE B 202 N ILE B 195 SHEET 7 B 7 ILE B 213 PRO B 214 -1 O ILE B 213 N LEU B 203 SHEET 1 C 7 PHE C 141 GLU C 144 0 SHEET 2 C 7 LEU C 165 ASP C 169 -1 N ILE C 166 O LEU C 143 SHEET 3 C 7 CYS C 219 GLN C 229 -1 O LYS C 224 N ASP C 169 SHEET 4 C 7 PHE C 179 LEU C 184 -1 O PHE C 179 N VAL C 225 SHEET 5 C 7 PHE C 189 ILE C 195 -1 O THR C 190 N ALA C 182 SHEET 6 C 7 PHE C 202 GLN C 204 -1 O PHE C 202 N ILE C 195 SHEET 7 C 7 ILE C 213 PRO C 214 -1 O ILE C 213 N LEU C 203 SHEET 1 D 7 PHE D 141 GLU D 144 0 SHEET 2 D 7 LEU D 165 ASP D 169 -1 N ILE D 166 O LEU D 143 SHEET 3 D 7 CYS D 219 GLN D 229 -1 O LYS D 224 N ASP D 169 SHEET 4 D 7 PHE D 179 LEU D 184 -1 O PHE D 179 N VAL D 225 SHEET 5 D 7 PHE D 189 ILE D 195 -1 O THR D 190 N ALA D 182 SHEET 6 D 7 PHE D 202 GLN D 204 -1 O PHE D 202 N ILE D 195 SHEET 7 D 7 ILE D 213 PRO D 214 -1 O ILE D 213 N LEU D 203

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