HEADER DE NOVO PROTEIN 14-FEB-14 4OZC TITLE BACKBONE MODIFICATIONS IN THE PROTEIN GB1 HELIX AND LOOPS: BETA- TITLE 2 ACPC21, BETA-ACPC24, BETA-3-LYS28, BETA-3-LYS31, BETA-ACPC35, BETA- TITLE 3 ACPC40 COMPND MOL_ID: 1; COMPND 2 MOLECULE: STREPTOCOCCAL PROTEIN GB1 BACKBONE MODIFIED VARIANT: BETA- COMPND 3 ACPC21, BETA-ACPC24, BETA-3-LYS28, BETA-3-LYS31, BETA-ACPC35, BETA- COMPND 4 ACPC40; COMPND 5 CHAIN: A; COMPND 6 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 7 15-NOV-23 4OZC 1 ATOM REVDAT 6 27-SEP-23 4OZC 1 REMARK REVDAT 5 22-NOV-17 4OZC 1 SOURCE REMARK REVDAT 4 25-FEB-15 4OZC 1 REMARK REVDAT 3 24-DEC-14 4OZC 1 DBREF REVDAT 2 24-SEP-14 4OZC 1 JRNL REVDAT 1 16-JUL-14 4OZC 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. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.490 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 3236 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.330 REMARK 3 FREE R VALUE TEST SET COUNT : 140 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 - 2.3005 0.98 3096 140 0.2171 0.2529 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.650 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.78 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 : 0.004 465 REMARK 3 ANGLE : 1.046 633 REMARK 3 CHIRALITY : 0.043 74 REMARK 3 PLANARITY : 0.002 75 REMARK 3 DIHEDRAL : 14.020 130 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 4OZC 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_1000200311. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 : 3245 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 28.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 5.310 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.46 REMARK 200 R MERGE FOR SHELL (I) : 0.35200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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 (%): 56.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 8.5, 2.0 M AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, HANGING 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 39.63950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 39.63950 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 11.26050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.63950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 5.63025 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.63950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 16.89075 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 39.63950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.63950 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 11.26050 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 39.63950 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 16.89075 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 39.63950 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 5.63025 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: 690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 OE1 GLU A 19 O HOH A 201 2.18 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 XCP A 40 C - N - CA ANGL. DEV. = 20.8 DEGREES 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 ALA A 20 XCP A 21 135.89 REMARK 500 ALA A 23 XCP A 24 139.23 REMARK 500 B3K A 28 VAL A 29 142.94 REMARK 500 B3K A 31 GLN A 32 146.15 REMARK 500 ALA A 34 XCP A 35 138.61 REMARK 500 VAL A 39 XCP A 40 141.80 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 B3K A 28 -18.18 REMARK 500 B3K A 31 -17.02 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 SO4 A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 103 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4OZA RELATED DB: PDB REMARK 900 RELATED ID: 4OZB RELATED DB: PDB DBREF 4OZC A 1 57 PDB 4OZC 4OZC 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 XCP ASP ALA XCP THR ALA SEQRES 3 A 57 GLU B3K VAL PHE B3K GLN TYR ALA XCP ASP ASN GLY VAL SEQRES 4 A 57 XCP GLY GLU TRP THR TYR ASP ASP ALA THR LYS THR PHE SEQRES 5 A 57 THR VAL THR GLU NH2 HET XCP A 21 8 HET XCP A 24 8 HET B3K A 28 10 HET B3K A 31 10 HET XCP A 35 8 HET XCP A 40 8 HET NH2 A 57 1 HET SO4 A 101 5 HET SO4 A 102 5 HET GOL A 103 6 HETNAM XCP (1S,2S)-2-AMINOCYCLOPENTANECARBOXYLIC ACID HETNAM B3K (3S)-3,7-DIAMINOHEPTANOIC ACID HETNAM NH2 AMINO GROUP HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 XCP 4(C6 H11 N O2) FORMUL 1 B3K 2(C7 H16 N2 O2) FORMUL 1 NH2 H2 N FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *19(H2 O) HELIX 1 AA1 ASP A 22 ASN A 37 1 16 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 20 N XCP A 21 1555 1555 1.32 LINK C XCP A 21 N ASP A 22 1555 1555 1.33 LINK C ALA A 23 N XCP A 24 1555 1555 1.33 LINK C XCP A 24 N THR A 25 1555 1555 1.33 LINK C GLU A 27 N B3K A 28 1555 1555 1.33 LINK C B3K A 28 N VAL A 29 1555 1555 1.33 LINK C PHE A 30 N B3K A 31 1555 1555 1.32 LINK C B3K A 31 N GLN A 32 1555 1555 1.33 LINK C ALA A 34 N XCP A 35 1555 1555 1.33 LINK C XCP A 35 N ASP A 36 1555 1555 1.33 LINK C VAL A 39 N XCP A 40 1555 1555 1.33 LINK C XCP A 40 N GLY A 41 1555 1555 1.33 LINK C GLU A 56 N NH2 A 57 1555 1555 1.33 SITE 1 AC1 5 GLU A 19 GLU A 27 B3K A 31 TRP A 43 SITE 2 AC1 5 HOH A 209 SITE 1 AC2 3 THR A 2 HOH A 202 HOH A 206 SITE 1 AC3 4 XCP A 40 GLY A 41 GLU A 56 NH2 A 57 CRYST1 79.279 79.279 22.521 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 0.012614 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012614 0.000000 0.00000 SCALE3 0.000000 0.000000 0.044402 0.00000