HEADER PEPTIDE BINDING PROTEIN 06-SEP-13 4MLS TITLE CRYSTAL STRUCTURE OF THE SPYTAG AND SPYCATCHER-DELTAN1 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: FIBRONECTIN BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 461-552; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: SPYTAG; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PYOGENES; SOURCE 3 ORGANISM_TAXID: 1314; SOURCE 4 GENE: CNAB2, FBA2; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: C43(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PDEST14; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS ISOPEPTIDE BOND, SPYCATCHER, PROTEIN ENGINEERING, PEPTIDE BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.LI,J.O.FIERER,T.A.RAPOPORT,M.HOWARTH REVDAT 4 06-NOV-24 4MLS 1 REMARK REVDAT 3 20-SEP-23 4MLS 1 SEQADV LINK REVDAT 2 22-JAN-14 4MLS 1 JRNL REVDAT 1 13-NOV-13 4MLS 0 JRNL AUTH L.LI,J.O.FIERER,T.A.RAPOPORT,M.HOWARTH JRNL TITL STRUCTURAL ANALYSIS AND OPTIMIZATION OF THE COVALENT JRNL TITL 2 ASSOCIATION BETWEEN SPYCATCHER AND A PEPTIDE TAG. JRNL REF J.MOL.BIOL. V. 426 309 2014 JRNL REFN ISSN 0022-2836 JRNL PMID 24161952 JRNL DOI 10.1016/J.JMB.2013.10.021 REMARK 2 REMARK 2 RESOLUTION. 1.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.7 REMARK 3 NUMBER OF REFLECTIONS : 5508 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.470 REMARK 3 FREE R VALUE TEST SET COUNT : 246 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 39.4022 - 2.4993 0.93 2714 118 0.1940 0.2041 REMARK 3 2 2.4993 - 1.9840 0.90 2548 128 0.2618 0.3388 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.70 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 : 0.008 745 REMARK 3 ANGLE : 1.111 1014 REMARK 3 CHIRALITY : 0.073 116 REMARK 3 PLANARITY : 0.005 129 REMARK 3 DIHEDRAL : 12.086 267 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 81.6837 49.9246 12.1716 REMARK 3 T TENSOR REMARK 3 T11: 0.2866 T22: 0.2108 REMARK 3 T33: 0.1496 T12: 0.0148 REMARK 3 T13: -0.0608 T23: 0.0212 REMARK 3 L TENSOR REMARK 3 L11: 6.9022 L22: 4.5359 REMARK 3 L33: 2.4570 L12: 2.6094 REMARK 3 L13: -0.8709 L23: 0.0054 REMARK 3 S TENSOR REMARK 3 S11: -0.0550 S12: 0.2449 S13: 0.0921 REMARK 3 S21: -0.3125 S22: 0.0689 S23: 0.2308 REMARK 3 S31: 0.1182 S32: 0.0212 S33: -0.0073 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): 88.4821 55.3086 3.6921 REMARK 3 T TENSOR REMARK 3 T11: 0.3927 T22: 0.4680 REMARK 3 T33: 0.1884 T12: -0.0044 REMARK 3 T13: -0.0402 T23: 0.0241 REMARK 3 L TENSOR REMARK 3 L11: 3.1862 L22: 4.8235 REMARK 3 L33: 2.7936 L12: 0.1353 REMARK 3 L13: 0.8133 L23: 2.0041 REMARK 3 S TENSOR REMARK 3 S11: 0.1513 S12: 0.2173 S13: -0.0174 REMARK 3 S21: -0.4093 S22: -0.0254 S23: -0.3179 REMARK 3 S31: -0.1242 S32: 0.5686 S33: -0.0772 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 4MLS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1000082070. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97920 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 : 5530 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.984 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.11700 REMARK 200 R SYM (I) : 0.11700 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) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.36200 REMARK 200 R SYM FOR SHELL (I) : 0.36200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.200 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: PDB ENTRY 2X5P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM ACETATE 0.1M PH4.5, NACL 200MM, REMARK 280 PEG3350 30%, GLYCEROL 5%, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295KK REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 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 3555 X+1/2,Y+1/2,Z 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 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 SMTRY1 3 1.000000 0.000000 0.000000 35.56450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.23700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.56450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.23700 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: 1690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 201 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 19 REMARK 465 SER A 20 REMARK 465 GLY A 21 REMARK 465 ASP A 22 REMARK 465 GLY A 104 REMARK 465 LYS A 105 REMARK 465 ALA A 106 REMARK 465 THR A 107 REMARK 465 LYS A 108 REMARK 465 GLY A 109 REMARK 465 ASP A 110 REMARK 465 ALA A 111 REMARK 465 HIS A 112 REMARK 465 ILE A 113 REMARK 465 LYS B 123 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 B 201 O HOH B 206 1.94 REMARK 500 OE1 GLN A 99 O HOH A 233 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NZ LYS A 52 OD1 ASP A 82 4746 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4MLI RELATED DB: PDB DBREF 4MLS A 22 113 UNP Q8G9G1 Q8G9G1_STRPY 461 552 DBREF 4MLS B 111 123 PDB 4MLS 4MLS 111 123 SEQADV 4MLS GLY A 19 UNP Q8G9G1 EXPRESSION TAG SEQADV 4MLS SER A 20 UNP Q8G9G1 EXPRESSION TAG SEQADV 4MLS GLY A 21 UNP Q8G9G1 EXPRESSION TAG SEQADV 4MLS GLU A 34 UNP Q8G9G1 ILE 473 ENGINEERED MUTATION SEQADV 4MLS TYR A 69 UNP Q8G9G1 MET 508 ENGINEERED MUTATION SEQRES 1 A 95 GLY SER GLY ASP SER ALA THR HIS ILE LYS PHE SER LYS SEQRES 2 A 95 ARG ASP GLU ASP GLY LYS GLU LEU ALA GLY ALA THR MET SEQRES 3 A 95 GLU LEU ARG ASP SER SER GLY LYS THR ILE SER THR TRP SEQRES 4 A 95 ILE SER ASP GLY GLN VAL LYS ASP PHE TYR LEU TYR PRO SEQRES 5 A 95 GLY LYS TYR THR PHE VAL GLU THR ALA ALA PRO ASP GLY SEQRES 6 A 95 TYR GLU VAL ALA THR ALA ILE THR PHE THR VAL ASN GLU SEQRES 7 A 95 GLN GLY GLN VAL THR VAL ASN GLY LYS ALA THR LYS GLY SEQRES 8 A 95 ASP ALA HIS ILE SEQRES 1 B 13 ALA HIS ILE VAL MET VAL ASP ALA TYR LYS PRO THR LYS FORMUL 3 HOH *61(H2 O) SHEET 1 A 3 LYS A 64 LEU A 68 0 SHEET 2 A 3 THR A 25 ARG A 32 -1 N ILE A 27 O PHE A 66 SHEET 3 A 3 HIS B 112 VAL B 116 1 O ILE B 113 N LYS A 28 SHEET 1 B 5 THR A 53 ILE A 58 0 SHEET 2 B 5 THR A 43 ASP A 48 -1 N LEU A 46 O ILE A 54 SHEET 3 B 5 GLY A 71 ALA A 79 -1 O VAL A 76 N GLU A 45 SHEET 4 B 5 ILE A 90 VAL A 94 -1 O PHE A 92 N TYR A 73 SHEET 5 B 5 VAL A 100 VAL A 102 -1 O THR A 101 N THR A 93 LINK NZ LYS A 31 CG ASP B 117 1555 1555 1.34 CRYST1 71.129 30.474 39.878 90.00 98.93 90.00 C 1 2 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 0.014059 0.000000 0.002210 0.00000 SCALE2 0.000000 0.032815 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025384 0.00000