HEADER DE NOVO PROTEIN 14-FEB-14 4OZA TITLE BACKBONE MODIFICATIONS IN THE PROTEIN GB1 HELIX: BETA-3-ALA24, BETA-3- TITLE 2 LYS28, BETA-3-GLN32, BETA-3-ASP36 COMPND MOL_ID: 1; COMPND 2 MOLECULE: STREPTOCOCCAL PROTEIN GB1 BACKBONE MODIFIED VARIANT: BETA- COMPND 3 3-ALA24, BETA-3-LYS28, BETA-3-GLN32, BETA-3-ASP36; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: STREPTOCOCCUS SP.; SOURCE 4 ORGANISM_TAXID: 1306 KEYWDS UNNATURAL BACKBONE, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Z.E.REINERT,W.S.HORNE REVDAT 9 10-JUL-24 4OZA 1 REMARK REVDAT 8 15-NOV-23 4OZA 1 ATOM REVDAT 7 27-SEP-23 4OZA 1 REMARK REVDAT 6 21-MAR-18 4OZA 1 REMARK REVDAT 5 22-NOV-17 4OZA 1 SOURCE REMARK REVDAT 4 25-FEB-15 4OZA 1 REMARK REVDAT 3 24-DEC-14 4OZA 1 DBREF REVDAT 2 24-SEP-14 4OZA 1 JRNL REVDAT 1 16-JUL-14 4OZA 0 JRNL AUTH Z.E.REINERT,W.S.HORNE JRNL TITL FOLDING THERMODYNAMICS OF PROTEIN-LIKE OLIGOMERS WITH JRNL TITL 2 HETEROGENEOUS BACKBONES. JRNL REF CHEM SCI V. 5 3325 2014 JRNL REFN ISSN 2041-6520 JRNL PMID 25071931 JRNL DOI 10.1039/C4SC01094A REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.480 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 2411 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.235 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.310 REMARK 3 FREE R VALUE TEST SET COUNT : 104 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 0.0000 - 2.2010 0.96 2307 104 0.2334 0.2600 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.470 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.01 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 457 REMARK 3 ANGLE : 1.139 620 REMARK 3 CHIRALITY : 0.089 73 REMARK 3 PLANARITY : 0.003 78 REMARK 3 DIHEDRAL : 15.327 140 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4OZA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-FEB-14. REMARK 100 THE DEPOSITION ID IS D_1000200309. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-AUG-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : RIGAKU VARIMAX OPTICS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2418 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 23.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 5.460 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.42 REMARK 200 R MERGE FOR SHELL (I) : 0.29600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CRYSTALCLEAR, PHASER REMARK 200 STARTING MODEL: 2QMT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M CALCIUM CHLORIDE, 0.1 M SODIUM REMARK 280 ACETATE PH 4.6, 30% V/V ISOPROPANOL, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 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 32.97200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 32.97200 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 10.94800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 32.97200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 5.47400 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 32.97200 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 16.42200 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 32.97200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 32.97200 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 10.94800 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 32.97200 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 16.42200 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 32.97200 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 5.47400 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 3.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 O HOH A 211 O HOH A 214 1.70 REMARK 500 OD1 ASN A 37 O HOH A 201 1.86 REMARK 500 O HOH A 216 O HOH A 236 2.13 REMARK 500 O HOH A 223 O HOH A 224 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 8 77.87 -100.58 REMARK 500 REMARK 500 REMARK: NULL 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 B3A A 24 THR A 25 141.20 REMARK 500 B3K A 28 VAL A 29 143.39 REMARK 500 B3Q A 32 TYR A 33 141.97 REMARK 500 B3D A 36 ASN A 37 145.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 B3A A 24 -18.97 REMARK 500 B3K A 28 -18.23 REMARK 500 B3Q A 32 -19.16 REMARK 500 B3D A 36 -16.07 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 IPA A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4OZB RELATED DB: PDB REMARK 900 RELATED ID: 4OZC RELATED DB: PDB DBREF 4OZA A 1 57 PDB 4OZA 4OZA 1 57 SEQRES 1 A 57 ASP THR TYR LYS LEU ILE LEU ASN GLY LYS THR LEU LYS SEQRES 2 A 57 GLY GLU THR THR THR GLU ALA VAL ASP ALA B3A THR ALA SEQRES 3 A 57 GLU B3K VAL PHE LYS B3Q TYR ALA ASN B3D ASN GLY VAL SEQRES 4 A 57 ASP GLY GLU TRP THR TYR ASP ASP ALA THR LYS THR PHE SEQRES 5 A 57 THR VAL THR GLU NH2 HET B3A A 24 6 HET B3K A 28 10 HET B3Q A 32 10 HET B3D A 36 9 HET NH2 A 57 1 HET IPA A 101 8 HETNAM B3A (3S)-3-AMINOBUTANOIC ACID HETNAM B3K (3S)-3,7-DIAMINOHEPTANOIC ACID HETNAM B3Q (3S)-3,6-DIAMINO-6-OXOHEXANOIC ACID HETNAM B3D 3-AMINOPENTANEDIOIC ACID HETNAM NH2 AMINO GROUP HETNAM IPA ISOPROPYL ALCOHOL HETSYN B3Q (S)-BETA-3-HOMOGLUTAMINE HETSYN B3D BETA-HOMOASPARTATE HETSYN IPA 2-PROPANOL FORMUL 1 B3A C4 H9 N O2 FORMUL 1 B3K C7 H16 N2 O2 FORMUL 1 B3Q C6 H12 N2 O3 FORMUL 1 B3D C5 H9 N O4 FORMUL 1 NH2 H2 N FORMUL 2 IPA C3 H8 O FORMUL 3 HOH *37(H2 O) HELIX 1 AA1 ASP A 22 GLY A 38 1 17 HELIX 2 AA2 ASP A 47 THR A 49 5 3 SHEET 1 AA1 4 LYS A 13 GLU A 19 0 SHEET 2 AA1 4 THR A 2 ASN A 8 -1 N LEU A 7 O GLY A 14 SHEET 3 AA1 4 THR A 51 THR A 55 1 O PHE A 52 N LYS A 4 SHEET 4 AA1 4 GLU A 42 ASP A 46 -1 N GLU A 42 O THR A 55 LINK C ALA A 23 N B3A A 24 1555 1555 1.33 LINK C B3A A 24 N THR A 25 1555 1555 1.34 LINK C GLU A 27 N B3K A 28 1555 1555 1.32 LINK C B3K A 28 N VAL A 29 1555 1555 1.33 LINK C LYS A 31 N B3Q A 32 1555 1555 1.33 LINK C B3Q A 32 N TYR A 33 1555 1555 1.33 LINK C ASN A 35 N B3D A 36 1555 1555 1.34 LINK C B3D A 36 N ASN A 37 1555 1555 1.33 LINK C GLU A 56 N NH2 A 57 1555 1555 1.23 SITE 1 AC1 5 GLU A 19 ALA A 20 VAL A 21 GLU A 27 SITE 2 AC1 5 TRP A 43 CRYST1 65.944 65.944 21.896 90.00 90.00 90.00 I 41 8 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 0.015164 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015164 0.000000 0.00000 SCALE3 0.000000 0.000000 0.045670 0.00000