HEADER DE NOVO PROTEIN 20-OCT-98 1BYZ TITLE DESIGNED PEPTIDE ALPHA-1, P1 FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (SYNTHETIC DESIGNED PEPTIDE "ALPHA-1"); COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: N TERMINI ARE ACETYLATED SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS HELICAL BILAYER; BIOMATERIAL, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.G.PRIVE,D.H.ANDERSON,L.WESSON,D.CASCIO,D.EISENBERG REVDAT 9 20-NOV-24 1BYZ 1 REMARK REVDAT 8 03-APR-24 1BYZ 1 REMARK REVDAT 7 15-NOV-23 1BYZ 1 REMARK LINK ATOM REVDAT 6 30-MAY-18 1BYZ 1 COMPND SOURCE REMARK REVDAT 5 04-OCT-17 1BYZ 1 REMARK REVDAT 4 13-JUL-11 1BYZ 1 VERSN REVDAT 3 24-FEB-09 1BYZ 1 VERSN REVDAT 2 22-DEC-99 1BYZ 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 28-OCT-98 1BYZ 0 JRNL AUTH G.G.PRIVE,D.H.ANDERSON,L.WESSON,D.CASCIO,D.EISENBERG JRNL TITL PACKED PROTEIN BILAYERS IN THE 0.90 A RESOLUTION STRUCTURE JRNL TITL 2 OF A DESIGNED ALPHA HELICAL BUNDLE. JRNL REF PROTEIN SCI. V. 8 1400 1999 JRNL REFN ISSN 0961-8368 JRNL PMID 10422828 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH W.R.PATTERSON,D.H.ANDERSON,W.F.DEGRADO,D.CASCIO,D.EISENBERG REMARK 1 TITL CENTROSYMMETRIC BILAYERS IN THE 0.75A RESOLUTION STRUCTURE REMARK 1 TITL 2 OF A DESIGNED ALPHA- HELICAL PEPTIDE, D, L-ALPHA-1 REMARK 1 REF PROTEIN SCI. V. 8 1410 1999 REMARK 1 REFN ISSN 0961-8368 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 AUTH 2 W.F.DE GRADO 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. 0.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 85.9 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : EVERY TENTH REFLECTION SAME REMARK 3 TEST SET FOR SHELXL-93 AND REMARK 3 SHELXL-97 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.086 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.085 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.105 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2368 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 23681 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.081 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.080 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.098 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 9.200 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 2179 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 21831 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 408 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 41 REMARK 3 SOLVENT ATOMS : 30 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 478.97 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 544.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 7 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 4695 REMARK 3 NUMBER OF RESTRAINTS : 5898 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.025 REMARK 3 ANGLE DISTANCES (A) : 0.000 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.016 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.017 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.065 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.192 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.006 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.026 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.108 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: ETHANOLAMINE AND MPD RESTRAINTS WERE DERIVED BY REMARK 3 ANALOGY TO OTHER SIMILAR GROUPS REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 MORE LOW-OCCUPANCY DISCRETE DISORDER COULD BE BUILT FOR SOLVENT REMARK 3 AND PEPTIDE, REMARK 3 BUT WOULD EXCESSIVELY INCREASE THE NUMBER OF REFINEABLE PARAMETERS. REMARK 4 REMARK 4 1BYZ 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_1000008155. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-94 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.0 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 (DENZO) REMARK 200 DATA SCALING SOFTWARE : SCALEPACK (DENZO) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23681 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.900 REMARK 200 RESOLUTION RANGE LOW (A) : 25.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.9 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07600 REMARK 200 FOR THE DATA SET : 16.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 36.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.14100 REMARK 200 FOR SHELL : 4.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: DIRECT METHODS REMARK 200 SOFTWARE USED: SNB (SNB 1.5) MILLER REMARK 200 STARTING MODEL: 448 RANDOM ATOMS REMARK 200 REMARK 200 REMARK: SNB SUCCESS RATE WAS 5%. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 27.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 91% 2-METHYL-2,4-PENTANEDIOL, 78MM REMARK 280 TRIETHANOLAMINE-HCL PH8, 52MM ETHANOLAMINE-HCL PH9.75, PH 8.0, REMARK 280 VAPOR DIFFUSION, SITTING 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 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 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 HZ1 LYS C 304 HO ETA C 501 1.35 REMARK 500 O HOH D 624 O HOH D 628 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 MPD 513 IS BUILT IN TWO OVERLAPPING CONFORMATIONS. ALL THE REMARK 600 WATERS ARE IN SINGLE SITES. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL C 520 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD D 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ETA C 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ETA A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD D 512 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 513 DBREF 1BYZ A 100 112 PDB 1BYZ 1BYZ 100 112 DBREF 1BYZ B 200 212 PDB 1BYZ 1BYZ 200 212 DBREF 1BYZ C 300 312 PDB 1BYZ 1BYZ 300 312 DBREF 1BYZ D 400 412 PDB 1BYZ 1BYZ 400 412 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 SEQRES 1 C 13 ACE GLU LEU LEU LYS LYS LEU LEU GLU GLU LEU LYS GLY SEQRES 1 D 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 ACE C 300 6 HET ACE D 400 6 HET ETA A 502 12 HET MPD A 513 44 HET MPD B 511 22 HET CL C 520 1 HET ETA C 501 12 HET MRD D 510 22 HET MPD D 512 22 HETNAM ACE ACETYL GROUP HETNAM ETA ETHANOLAMINE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM CL CHLORIDE ION HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL FORMUL 1 ACE 4(C2 H4 O) FORMUL 5 ETA 2(C2 H7 N O) FORMUL 6 MPD 3(C6 H14 O2) FORMUL 8 CL CL 1- FORMUL 10 MRD C6 H14 O2 FORMUL 12 HOH *30(H2 O) HELIX 1 1 GLU A 101 GLY A 112 1 12 HELIX 2 2 GLU B 201 GLY B 212 1 12 HELIX 3 3 GLU C 301 GLY C 312 1 12 HELIX 4 4 GLU D 401 GLY D 412 1 12 LINK C ACE A 100 N GLU A 101 1555 1555 1.35 LINK C ACE B 200 N GLU B 201 1555 1555 1.33 LINK C ACE C 300 N GLU C 301 1555 1555 1.35 LINK C ACE D 400 N GLU D 401 1555 1555 1.36 SITE 1 AC1 4 LYS A 104 LYS B 204 LYS C 311 LYS D 405 SITE 1 AC2 4 ACE D 400 LEU D 402 LEU D 403 LEU D 410 SITE 1 AC3 6 GLU A 109 GLY A 112 HOH A 604 GLU C 301 SITE 2 AC3 6 LYS C 304 GLU C 308 SITE 1 AC4 4 LYS A 105 GLY A 112 GLU B 209 GLY C 312 SITE 1 AC5 3 LEU A 103 LEU B 210 MPD D 512 SITE 1 AC6 4 MPD B 511 LEU C 310 LEU D 402 GLU D 409 SITE 1 AC7 10 ACE A 100 LEU A 102 GLU A 109 LEU A 110 SITE 2 AC7 10 HOH A 619 LEU B 203 GLU B 209 HOH B 614 SITE 3 AC7 10 HOH B 633 LEU D 406 CRYST1 20.846 20.909 27.057 102.40 95.33 119.62 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 0.047971 0.027273 0.013306 0.00000 SCALE2 0.000000 0.055015 0.017373 0.00000 SCALE3 0.000000 0.000000 0.038926 0.00000 HETATM 1 C ACE A 100 5.817 -4.950 19.120 1.00 3.19 C ANISOU 1 C ACE A 100 352 461 401 84 -25 135 C HETATM 2 O ACE A 100 4.606 -5.067 18.914 1.00 3.61 O ANISOU 2 O ACE A 100 329 468 575 45 -96 52 O HETATM 3 CH3 ACE A 100 6.849 -5.672 18.292 1.00 4.55 C ANISOU 3 CH3 ACE A 100 543 547 639 160 51 -2 C HETATM 4 H1 ACE A 100 7.745 -5.448 18.619 1.00 6.83 H ANISOU 4 H1 ACE A 100 865 865 865 0 0 0 H HETATM 5 H2 ACE A 100 6.766 -5.398 17.355 1.00 6.83 H ANISOU 5 H2 ACE A 100 865 865 865 0 0 0 H HETATM 6 H3 ACE A 100 6.707 -6.639 18.364 1.00 6.83 H ANISOU 6 H3 ACE A 100 865 865 865 0 0 0 H