HEADER BIOSYNTHETIC PROTEIN 28-FEB-20 6VZX TITLE STRUCTURE OF A COVALENTLY CAPTURED COLLAGEN TRIPLE HELIX USING LYSINE- TITLE 2 GLUTAMATE PAIRS COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLLAGEN MIMETIC PEPTIDE; COMPND 3 CHAIN: A, B, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 OTHER_DETAILS: FMOC SOLID PHASE PEPTIDE CHEMISTRY WITH N-TERMINAL SOURCE 6 ACETYLATION AND C-TERMINAL AMIDATION KEYWDS COLLAGEN MIMETIC PEPTIDE, TRIPLE HELIX, ISOPEPTIDE BOND, BIOSYNTHETIC KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.D.MILLER,S.A.HULGAN,W.XU,A.J.KOSGEI,G.N.PHILLIPS JR.,J.D.HARTGERINK REVDAT 3 11-OCT-23 6VZX 1 REMARK REVDAT 2 30-SEP-20 6VZX 1 JRNL REVDAT 1 02-SEP-20 6VZX 0 JRNL AUTH S.A.H.HULGAN,A.A.JALAN,I.C.LI,D.R.WALKER,M.D.MILLER, JRNL AUTH 2 A.J.KOSGEI,W.XU,G.N.PHILLIPS JR.,J.D.HARTGERINK JRNL TITL COVALENT CAPTURE OF COLLAGEN TRIPLE HELICES USING JRNL TITL 2 LYSINE-ASPARTATE AND LYSINE-GLUTAMATE PAIRS. JRNL REF BIOMACROMOLECULES V. 21 3772 2020 JRNL REFN ESSN 1526-4602 JRNL PMID 32820897 JRNL DOI 10.1021/ACS.BIOMAC.0C00878 REMARK 2 REMARK 2 RESOLUTION. 1.37 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 1.37 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 9539 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.850 REMARK 3 FREE R VALUE TEST SET COUNT : 463 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 33.7100 - 1.9800 1.00 3320 176 0.1340 0.1513 REMARK 3 2 1.9800 - 1.5700 1.00 3178 163 0.1820 0.2124 REMARK 3 3 1.5700 - 1.3700 0.80 2578 124 0.2174 0.2454 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.08 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 : 0.013 531 REMARK 3 ANGLE : 1.661 747 REMARK 3 CHIRALITY : 0.052 71 REMARK 3 PLANARITY : 0.008 105 REMARK 3 DIHEDRAL : 11.557 280 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 6VZX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1000247387. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-OCT-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL CRYO-COOLED REMARK 200 SI(111) REMARK 200 OPTICS : ADJUSTABLE FOCUS K-B PAIR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 0.5.893-GB176367E-DIALS REMARK 200 -1.14, DIALS 1.14.5-G19190E3B9- REMARK 200 RELEASE REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9559 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.370 REMARK 200 RESOLUTION RANGE LOW (A) : 33.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 200 DATA REDUNDANCY : 11.20 REMARK 200 R MERGE (I) : 0.14900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.37 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 59.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 1.01400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: 3T4F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 29.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.5 M SODIUM FORMATE, 0.1 M BIS-TRIS, REMARK 280 PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 67.41750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 7.05650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 67.41750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 7.05650 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 B 140 LIES ON A SPECIAL POSITION. 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 OD1 HYP A 23 O HOH A 101 1.99 REMARK 500 OD1 HYP C 23 O HOH C 101 2.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3T4F RELATED DB: PDB REMARK 900 KGE COLLAGEN MIMETIC PEPTIDE WITHOUT COVALENT CAPTURE REMARK 900 RELATED ID: 3U29 RELATED DB: PDB REMARK 900 KGD COLLAGEN MIMETIC PEPTIDE WITHOUT COVALENT CAPTURE DBREF 6VZX A 0 25 PDB 6VZX 6VZX 0 25 DBREF 6VZX B 0 25 PDB 6VZX 6VZX 0 25 DBREF 6VZX C 0 25 PDB 6VZX 6VZX 0 25 SEQRES 1 A 26 ACE PRO HYP GLY PRO HYP GLY PRO HYP GLY PRO LYS GLY SEQRES 2 A 26 GLU HYP GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY NH2 SEQRES 1 B 26 ACE PRO HYP GLY PRO HYP GLY PRO HYP GLY PRO LYS GLY SEQRES 2 B 26 GLU HYP GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY NH2 SEQRES 1 C 26 ACE PRO HYP GLY PRO HYP GLY PRO HYP GLY PRO LYS GLY SEQRES 2 C 26 GLU HYP GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY NH2 HET ACE A 0 6 HET HYP A 2 15 HET HYP A 5 15 HET HYP A 8 15 HET HYP A 14 15 HET HYP A 17 15 HET HYP A 20 15 HET HYP A 23 15 HET NH2 A 25 3 HET ACE B 0 6 HET HYP B 2 15 HET HYP B 5 15 HET HYP B 8 15 HET HYP B 14 15 HET HYP B 17 15 HET HYP B 20 15 HET HYP B 23 15 HET NH2 B 25 3 HET ACE C 0 6 HET HYP C 2 15 HET HYP C 5 15 HET HYP C 8 15 HET HYP C 14 15 HET HYP C 17 15 HET HYP C 20 15 HET HYP C 23 15 HET NH2 C 25 3 HETNAM ACE ACETYL GROUP HETNAM HYP 4-HYDROXYPROLINE HETNAM NH2 AMINO GROUP HETSYN HYP HYDROXYPROLINE FORMUL 1 ACE 3(C2 H4 O) FORMUL 1 HYP 21(C5 H9 N O3) FORMUL 1 NH2 3(H2 N) FORMUL 4 HOH *136(H2 O) LINK C ACE A 0 N PRO A 1 1555 1555 1.35 LINK C PRO A 1 N HYP A 2 1555 1555 1.33 LINK C HYP A 2 N GLY A 3 1555 1555 1.32 LINK C PRO A 4 N HYP A 5 1555 1555 1.32 LINK C HYP A 5 N GLY A 6 1555 1555 1.32 LINK C PRO A 7 N HYP A 8 1555 1555 1.32 LINK C HYP A 8 N GLY A 9 1555 1555 1.33 LINK NZ LYS A 11 CD GLU B 13 1555 1555 1.33 LINK C GLU A 13 N HYP A 14 1555 1555 1.32 LINK CD GLU A 13 NZ LYS C 11 1555 1555 1.33 LINK C HYP A 14 N GLY A 15 1555 1555 1.34 LINK C PRO A 16 N HYP A 17 1555 1555 1.32 LINK C HYP A 17 N GLY A 18 1555 1555 1.33 LINK C APRO A 19 N HYP A 20 1555 1555 1.32 LINK C BPRO A 19 N HYP A 20 1555 1555 1.32 LINK C HYP A 20 N GLY A 21 1555 1555 1.33 LINK C PRO A 22 N HYP A 23 1555 1555 1.31 LINK C HYP A 23 N GLY A 24 1555 1555 1.33 LINK C GLY A 24 N NH2 A 25 1555 1555 1.32 LINK C ACE B 0 N PRO B 1 1555 1555 1.35 LINK C PRO B 1 N HYP B 2 1555 1555 1.33 LINK C HYP B 2 N GLY B 3 1555 1555 1.33 LINK C PRO B 4 N HYP B 5 1555 1555 1.32 LINK C HYP B 5 N GLY B 6 1555 1555 1.32 LINK C PRO B 7 N HYP B 8 1555 1555 1.32 LINK C HYP B 8 N GLY B 9 1555 1555 1.33 LINK NZ LYS B 11 CD GLU C 13 1555 1555 1.33 LINK C GLU B 13 N HYP B 14 1555 1555 1.32 LINK C HYP B 14 N GLY B 15 1555 1555 1.33 LINK C PRO B 16 N HYP B 17 1555 1555 1.32 LINK C HYP B 17 N GLY B 18 1555 1555 1.32 LINK C PRO B 19 N HYP B 20 1555 1555 1.31 LINK C HYP B 20 N GLY B 21 1555 1555 1.32 LINK C PRO B 22 N HYP B 23 1555 1555 1.33 LINK C HYP B 23 N GLY B 24 1555 1555 1.33 LINK C GLY B 24 N NH2 B 25 1555 1555 1.32 LINK C ACE C 0 N PRO C 1 1555 1555 1.35 LINK C PRO C 1 N HYP C 2 1555 1555 1.32 LINK C HYP C 2 N GLY C 3 1555 1555 1.33 LINK C APRO C 4 N HYP C 5 1555 1555 1.32 LINK C BPRO C 4 N HYP C 5 1555 1555 1.32 LINK C HYP C 5 N GLY C 6 1555 1555 1.33 LINK C PRO C 7 N HYP C 8 1555 1555 1.33 LINK C HYP C 8 N GLY C 9 1555 1555 1.32 LINK C GLU C 13 N HYP C 14 1555 1555 1.32 LINK C HYP C 14 N GLY C 15 1555 1555 1.32 LINK C PRO C 16 N HYP C 17 1555 1555 1.32 LINK C HYP C 17 N GLY C 18 1555 1555 1.33 LINK C PRO C 19 N HYP C 20 1555 1555 1.32 LINK C HYP C 20 N GLY C 21 1555 1555 1.33 LINK C PRO C 22 N HYP C 23 1555 1555 1.33 LINK C HYP C 23 N GLY C 24 1555 1555 1.32 LINK C GLY C 24 N NH2 C 25 1555 1555 1.33 CRYST1 134.835 14.113 24.568 90.00 90.35 90.00 C 1 2 1 12 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 0.007416 0.000000 0.000045 0.00000 SCALE2 0.000000 0.070857 0.000000 0.00000 SCALE3 0.000000 0.000000 0.040704 0.00000 HETATM 1 C ACE A 0 -7.601 9.533 19.235 1.00 33.58 C HETATM 2 O ACE A 0 -7.380 8.481 18.653 1.00 24.70 O HETATM 3 CH3 ACE A 0 -8.639 9.642 20.302 1.00 23.13 C HETATM 4 H1 ACE A 0 -8.353 9.153 21.232 1.00 27.73 H HETATM 5 H2 ACE A 0 -9.592 9.197 20.022 1.00 27.73 H HETATM 6 H3 ACE A 0 -8.869 10.671 20.575 1.00 27.73 H