HEADER HYDROLASE 26-FEB-15 4YGW TITLE RNASE S IN COMPLEX WITH STABILIZED S PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: S-PEPTIDE: ACE-LYS-GLU-THR-ALA-ALA-HCS-LYS-PHE-GLU-HCS-GLN- COMPND 3 HIS-MET-ASP-SER; COMPND 4 CHAIN: b; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RIBONUCLEASE A C2; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: UNP RESIDUES 113-215; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 7 ORGANISM_COMMON: BOVINE; SOURCE 8 ORGANISM_TAXID: 9913; SOURCE 9 ORGAN: PANCREAS; SOURCE 10 GENE: RAC2; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RNASE, UNNATURAL AMINO ACIDS, SIDE CHAIN LINK, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR N.ASSEM,D.FERREIRA,D.W.WOLAN,P.E.DAWSON REVDAT 7 03-APR-24 4YGW 1 HETSYN REVDAT 6 15-NOV-23 4YGW 1 REMARK REVDAT 5 27-SEP-23 4YGW 1 REMARK REVDAT 4 30-MAR-22 4YGW 1 SOURCE JRNL REMARK LINK REVDAT 3 29-JUL-15 4YGW 1 JRNL REVDAT 2 08-JUL-15 4YGW 1 SOURCE KEYWDS REVDAT 1 01-JUL-15 4YGW 0 JRNL AUTH N.ASSEM,D.J.FERREIRA,D.W.WOLAN,P.E.DAWSON JRNL TITL ACETONE-LINKED PEPTIDES: A CONVERGENT APPROACH FOR PEPTIDE JRNL TITL 2 MACROCYCLIZATION AND LABELING. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 54 8665 2015 JRNL REFN ESSN 1521-3773 JRNL PMID 26096515 JRNL DOI 10.1002/ANIE.201502607 REMARK 2 REMARK 2 RESOLUTION. 2.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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) : 2.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.2 REMARK 3 NUMBER OF REFLECTIONS : 5804 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 290 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 40.2808 - 2.7413 0.99 3057 161 0.1913 0.2089 REMARK 3 2 2.7413 - 2.1800 0.84 2457 129 0.2321 0.2492 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.420 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.004 983 REMARK 3 ANGLE : 0.649 1330 REMARK 3 CHIRALITY : 0.025 144 REMARK 3 PLANARITY : 0.002 173 REMARK 3 DIHEDRAL : 14.733 368 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 4YGW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000207449. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JAN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97950 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5835 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.180 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.2 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.11500 REMARK 200 R SYM (I) : 0.09900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 58.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.37200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3OQY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE, PH 5.5, 27.5% REMARK 280 PEG4000, 0.06 M AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 14.28100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.71000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.55400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.71000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.28100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.55400 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: b, 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER B 22 OG 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 ASP b 15 71.25 -157.33 REMARK 500 GLN B 60 -150.53 -116.83 REMARK 500 ASN B 94 76.47 -101.02 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 B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues 4Y8 b 101 and HCS b 11 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues 4Y8 b 101 and HCS b 7 DBREF 4YGW b 1 16 PDB 4YGW 4YGW 1 16 DBREF 4YGW B 22 124 UNP W0UVI3 W0UVI3_BOVIN 113 215 SEQRES 1 b 16 ACE LYS GLU THR ALA ALA HCS LYS PHE GLU HCS GLN HIS SEQRES 2 b 16 MET ASP SER SEQRES 1 B 103 SER SER ASN TYR CYS ASN GLN MET MET LYS SER ARG ASN SEQRES 2 B 103 LEU THR LYS ASP ARG CYS LYS PRO VAL ASN THR PHE VAL SEQRES 3 B 103 HIS GLU SER LEU ALA ASP VAL GLN ALA VAL CYS SER GLN SEQRES 4 B 103 LYS ASN VAL ALA CYS LYS ASN GLY GLN THR ASN CYS TYR SEQRES 5 B 103 GLN SER TYR SER THR MET SER ILE THR ASP CYS ARG GLU SEQRES 6 B 103 THR GLY SER SER LYS TYR PRO ASN CYS ALA TYR LYS THR SEQRES 7 B 103 THR GLN ALA ASN LYS HIS ILE ILE VAL ALA CYS GLU GLY SEQRES 8 B 103 ASN PRO TYR VAL PRO VAL HIS PHE ASP ALA SER VAL HET ACE b 1 3 HET HCS b 7 7 HET HCS b 11 7 HET 4Y8 b 101 4 HET SO4 B 201 5 HET SO4 B 202 5 HETNAM ACE ACETYL GROUP HETNAM HCS 2-AMINO-4-MERCAPTO-BUTYRIC ACID HETNAM 4Y8 1-HYDROXYPROPAN-2-ONE HETNAM SO4 SULFATE ION HETSYN HCS L-HOMOCYSTEINE FORMUL 1 ACE C2 H4 O FORMUL 1 HCS 2(C4 H9 N O2 S) FORMUL 3 4Y8 C3 H6 O2 FORMUL 4 SO4 2(O4 S 2-) FORMUL 6 HOH *76(H2 O) HELIX 1 AA1 THR b 4 MET b 14 1 11 HELIX 2 AA2 ASN B 24 ARG B 33 1 10 HELIX 3 AA3 SER B 50 ALA B 56 1 7 HELIX 4 AA4 VAL B 57 GLN B 60 5 4 SHEET 1 AA1 3 VAL B 43 VAL B 47 0 SHEET 2 AA1 3 MET B 79 GLU B 86 -1 O THR B 82 N PHE B 46 SHEET 3 AA1 3 TYR B 97 LYS B 104 -1 O THR B 100 N ASP B 83 SHEET 1 AA2 4 LYS B 61 VAL B 63 0 SHEET 2 AA2 4 CYS B 72 GLN B 74 -1 O GLN B 74 N LYS B 61 SHEET 3 AA2 4 ILE B 106 GLU B 111 -1 O VAL B 108 N TYR B 73 SHEET 4 AA2 4 VAL B 116 SER B 123 -1 O ALA B 122 N ILE B 107 SSBOND 1 CYS B 26 CYS B 84 1555 1555 2.03 SSBOND 2 CYS B 40 CYS B 95 1555 1555 2.03 SSBOND 3 CYS B 58 CYS B 110 1555 1555 2.03 SSBOND 4 CYS B 65 CYS B 72 1555 1555 2.03 LINK C ACE b 1 N LYS b 2 1555 1555 1.33 LINK C ALA b 6 N HCS b 7 1555 1555 1.33 LINK C HCS b 7 N LYS b 8 1555 1555 1.33 LINK SD HCS b 7 CM2 4Y8 b 101 1555 1555 1.82 LINK C GLU b 10 N HCS b 11 1555 1555 1.33 LINK C HCS b 11 N GLN b 12 1555 1555 1.33 LINK SD HCS b 11 CM1 4Y8 b 101 1555 1555 1.70 CISPEP 1 TYR B 92 PRO B 93 0 3.65 CISPEP 2 ASN B 113 PRO B 114 0 5.56 SITE 1 AC1 7 LYS B 41 SER B 59 HIS B 119 PHE B 120 SITE 2 AC1 7 GLN b 12 HIS b 13 HOH b 203 SITE 1 AC2 3 LYS B 31 THR B 87 GLY B 88 SITE 1 AC3 9 ARG B 33 GLY B 68 GLU b 3 HCS b 7 SITE 2 AC3 9 LYS b 8 PHE b 9 GLU b 10 GLN b 12 SITE 3 AC3 9 HIS b 13 SITE 1 AC4 8 GLU b 3 THR b 4 ALA b 5 ALA b 6 SITE 2 AC4 8 LYS b 8 PHE b 9 GLU b 10 HCS b 11 CRYST1 28.562 87.108 45.420 90.00 90.00 90.00 P 21 21 21 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 0.035012 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011480 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022017 0.00000 HETATM 1 C ACE b 1 5.211 11.506 15.999 1.00 57.81 C HETATM 2 O ACE b 1 4.262 12.067 15.450 1.00 51.53 O HETATM 3 CH3 ACE b 1 5.645 11.853 17.393 1.00 61.90 C