HEADER STRUCTURAL PROTEIN 26-OCT-98 3AL1 TITLE DESIGNED PEPTIDE ALPHA-1, RACEMIC P1BAR FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (D, L-ALPHA-1); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: N TERMINI ARE ACETYLATED SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: PEPTIDE WAS SYNTHESIZED VIA SOLID PHASE SYNTHESIS AND SOURCE 4 DESIGNED TO BE AN AMPHIPHILIC HELIX KEYWDS HELICAL BILAYER, BIOMATERIAL, CENTRIC, RACEMIC, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR W.R.PATTERSON,D.H.ANDERSON,W.F.DEGRADO,D.CASCIO,D.EISENBERG REVDAT 8 03-APR-24 3AL1 1 REMARK REVDAT 7 15-NOV-23 3AL1 1 REMARK LINK ATOM REVDAT 6 28-MAR-12 3AL1 1 CRYST1 VERSN REVDAT 5 24-FEB-09 3AL1 1 VERSN REVDAT 4 01-APR-03 3AL1 1 JRNL REVDAT 3 26-SEP-01 3AL1 3 ATOM CONECT REVDAT 2 22-DEC-99 3AL1 1 HEADER COMPND REMARK JRNL REVDAT 2 2 1 ATOM SOURCE SEQRES REVDAT 1 04-NOV-98 3AL1 0 JRNL AUTH W.R.PATTERSON,D.H.ANDERSON,W.F.DEGRADO,D.CASCIO,D.EISENBERG JRNL TITL CENTROSYMMETRIC BILAYERS IN THE 0.75 A RESOLUTION STRUCTURE JRNL TITL 2 OF A DESIGNED ALPHA-HELICAL PEPTIDE, D,L-ALPHA-1. JRNL REF PROTEIN SCI. V. 8 1410 1999 JRNL REFN ISSN 0961-8368 JRNL PMID 10422829 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH G.G.PRIVE,D.H.ANDERSON,L.WESSON,D.CASCIO,D.EISENBERG REMARK 1 TITL PACKED PROTEIN BILAYERS IN THE 0.90A RESOLUTION STRUCTURE OF REMARK 1 TITL 2 A DESIGNED ALPHA HELICAL BUNDLE REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 1 REFERENCE 2 REMARK 1 AUTH C.P.HILL,D.H.ANDERSON,L.WESSON,W.F.DEGRADO,D.EISENBERG REMARK 1 TITL CRYSTAL STRUCTURE OF ALPHA-1: IMPLICATIONS FOR PROTEIN REMARK 1 TITL 2 DESIGN REMARK 1 REF SCIENCE V. 249 543 1990 REMARK 1 REFN ISSN 0036-8075 REMARK 1 REFERENCE 3 REMARK 1 AUTH D.EISENBERG,W.WILCOX,S.M.ESHITA,P.M.PRYCIAK,S.P.HO REMARK 1 TITL THE DESIGN, SYNTHESIS, AND CRYSTALLIZATION OF AN REMARK 1 TITL 2 ALPHA-HELICAL PEPTIDE REMARK 1 REF PROTEINS V. 1 16 1986 REMARK 1 REFN ISSN 0887-3585 REMARK 2 REMARK 2 RESOLUTION. 0.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 71.6 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : EVERY TENTH REFLECTION REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.131 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.130 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.145 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3329 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 33290 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.107 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.107 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.120 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 8.100 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 2419 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 24134 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 204 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 21 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 237.88 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 250.04 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 11 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 2939 REMARK 3 NUMBER OF RESTRAINTS : 4291 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.038 REMARK 3 ANGLE DISTANCES (A) : 0.000 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.028 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.017 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.101 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.086 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.007 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.038 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.040 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: GLU 108 CONFORMATION C CARBOXYLATE HAS A STIFF REMARK 3 PLANARITY RESTRAINT. ETHANOLAMINE AND MPD REMARK 3 RESTRAINTS WERE DERIVED BY ANALOGY TO OTHER REMARK 3 SIMILAR GROUPS. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 STRUCTURE WAS REDETERMINED WITH SHAKE AND BAKE BECAUSE THE REMARK 3 REFINEMENT WAS STUCK AT R ABOUT 21%. THE SNB RESULT REMARK 3 CONFIRMED THE SHELXS STRUCTURE. REMARK 3 REMARK 3 SAME TEST SET WAS USED FOR SHELXL-93 AND -97. SAME REMARK 3 RESTRAINTS WERE CARRIED ALONG INTO SHELXL-97; THERE WAS NO REMARK 3 DFIX/DANG DISTINCTION. REMARK 3 REMARK 3 INTRODUCTION OF ANISOTROPIC REFINEMENT REDUCED FREE R REMARK 3 (NO CUTOFF) BY ONLY 1%. IN THIS REFINEMENT, THE ALTERNATE REMARK 3 CONFORMATIONS EVENTUALLY REDUCED FREE R FROM 22.6 - 14.5% REMARK 4 REMARK 4 3AL1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE DEPOSITION ID IS D_1000008049. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-96 REMARK 200 TEMPERATURE (KELVIN) : 115 REMARK 200 PH : 8-9.75 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33573 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.750 REMARK 200 RESOLUTION RANGE LOW (A) : 18.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 71.5 REMARK 200 DATA REDUNDANCY : 1.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 10.0000 REMARK 200 FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 24.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: DIRECT METHODS REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THERE IS NO REDUNDANCY IN THE DATA REMARK 200 SET BEYOND 1.28A RESOLUTION; RSYM CAN BE EVALUATED ONLY FOR REMARK 200 18-1.28A. DATA REDUNDANCY IN 18-1.28A SHELL IS 2.51 REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 14.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: EQUAL VOLUMES OF 10 MG/ML D-ALPHA-1 REMARK 280 AND 10 MG/ML L-ALPHA-1 WERE MIXED IMMEDIATELY BEFORE REMARK 280 CRYSTALLIZATION. THE RESERVOIR SOLUTION CONTAINED 90-93% 2- REMARK 280 METHYL-2,4-PENTANEDIOL, 0.075 M ETHANOLAMINE HCL PH 9.75, 0.05 M REMARK 280 TRIETHANOLAMINE HCL PH 8. THE HANGING DROP CONTAINED EQUAL REMARK 280 VOLUMES OF RESERVOIR AND 10 MG/ML D,L MIX ALPHA-1. THE ACIDIC REMARK 280 PEPTIDE PARTWAY TITRATES THE BASIC BUFFERS TO REACH THE UNKNOWN REMARK 280 RESULTANT PH., VAPOR DIFFUSION - HANGING DROP, VAPOR DIFFUSION, REMARK 280 HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P -1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE2 GLU A 109 HZ1 LYS B 205 1.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS A 105 CG LYS A 105 CD -0.208 REMARK 500 GLU A 108 CG GLU A 108 CD 0.119 REMARK 500 GLU A 108 CD GLU A 108 OE2 -0.118 REMARK 500 GLU A 108 CD GLU A 108 OE2 0.092 REMARK 500 REMARK 500 REMARK: NULL 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 PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LYS A 105 CB - CG - CD ANGL. DEV. = 43.1 DEGREES REMARK 500 GLU A 108 OE1 - CD - OE2 ANGL. DEV. = 8.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ETA B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ETA B 506 DBREF 3AL1 A 100 112 PDB 3AL1 3AL1 100 112 DBREF 3AL1 B 200 212 PDB 3AL1 3AL1 200 212 SEQRES 1 A 13 ACE GLU LEU LEU LYS LYS LEU LEU GLU GLU LEU LYS GLY SEQRES 1 B 13 ACE GLU LEU LEU LYS LYS LEU LEU GLU GLU LEU LYS GLY HET ACE A 100 6 HET ACE B 200 6 HET MPD A 400 44 HET ETA B 501 8 HET ETA B 506 8 HETNAM ACE ACETYL GROUP HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM ETA ETHANOLAMINE FORMUL 1 ACE 2(C2 H4 O) FORMUL 3 MPD C6 H14 O2 FORMUL 4 ETA 2(C2 H7 N O) FORMUL 6 HOH *21(H2 O) HELIX 1 1 LEU A 102 LEU A 110 1 9 HELIX 2 2 LEU B 202 LEU B 210 1 9 LINK C ACE A 100 N GLU A 101 1555 1555 1.33 LINK C ACE B 200 N GLU B 201 1555 1555 1.33 SITE 1 AC1 6 LEU A 102 GLU A 109 LEU A 110 HOH A 303 SITE 2 AC1 6 LEU B 210 ETA B 501 SITE 1 AC2 8 GLU A 109 GLY A 112 HOH A 313 MPD A 400 SITE 2 AC2 8 GLU B 209 GLY B 212 HOH B 304 HOH B 327 SITE 1 AC3 6 GLU A 108 GLU A 109 HOH A 305 LYS B 205 SITE 2 AC3 6 HOH B 325 HOH B 327 CRYST1 20.544 20.859 26.055 101.16 97.03 118.06 P -1 4 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 0.048676 0.025947 0.014031 0.00000 SCALE2 0.000000 0.054327 0.016259 0.00000 SCALE3 0.000000 0.000000 0.040366 0.00000 HETATM 1 C ACE A 100 -3.325 -4.221 -7.090 1.00 4.77 C ANISOU 1 C ACE A 100 753 462 597 44 -154 40 C HETATM 2 O ACE A 100 -4.501 -4.405 -7.438 1.00 5.17 O ANISOU 2 O ACE A 100 737 525 702 11 -229 -20 O HETATM 3 CH3 ACE A 100 -2.187 -4.936 -7.721 1.00 5.68 C ANISOU 3 CH3 ACE A 100 891 620 647 99 -67 -42 C HETATM 4 H1 ACE A 100 -1.349 -4.649 -7.303 1.00 8.52 H ANISOU 4 H1 ACE A 100 1079 1079 1079 0 0 0 H HETATM 5 H2 ACE A 100 -2.163 -4.731 -8.679 1.00 8.52 H ANISOU 5 H2 ACE A 100 1079 1079 1079 0 0 0 H HETATM 6 H3 ACE A 100 -2.300 -5.902 -7.597 1.00 8.52 H ANISOU 6 H3 ACE A 100 1079 1079 1079 0 0 0 H