HEADER STRUCTURAL PROTEIN 17-JAN-25 9LLR TITLE THE DESIGNED COLLAGEN HETEROTRIMER PEPTIDES WITH VARIOUS STABILIZING TITLE 2 SIDE CHAIN PAIRS COMPND MOL_ID: 1; COMPND 2 MOLECULE: ABC TYPE HETEROTRIMER COLLAGEN-LIKE PEPTIDE CHAIN B; COMPND 3 CHAIN: B, E; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: COLLAGEN ALIGNMENT; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: ABC TYPE HETEROTRIMER COLLAGEN-LIKE PEPTIDE CHAIN C; COMPND 8 CHAIN: C, F; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: ABC TYPE HETEROTRIMER COLLAGEN-LIKE PEPTIDE CHAIN A; COMPND 12 CHAIN: A, D; COMPND 13 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 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630 KEYWDS COLLAGEN HETEROTRIMER, EXTRACELLULAR MATRIX, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.X.ZHANG,F.XU,S.L.FAN REVDAT 1 22-JUL-26 9LLR 0 JRNL AUTH R.X.ZHANG,C.G.QIU,R.ZSCHAU,M.ZACHARIAS,S.L.FAN,V.NANDA,F.XU JRNL TITL DESIGN OF HETEROSPECIFIC COLLAGENS DIRECTED BY CHEMICALLY JRNL TITL 2 DIVERSE SURFACE INTERACTIONS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 27562 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.810 REMARK 3 FREE R VALUE TEST SET COUNT : 1325 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 23.5080 - 3.0215 0.98 3125 148 0.1845 0.2235 REMARK 3 2 3.0215 - 2.3990 0.98 2986 165 0.1814 0.2104 REMARK 3 3 2.3990 - 2.0960 0.97 2958 148 0.1572 0.1877 REMARK 3 4 2.0960 - 1.9045 0.97 2948 153 0.1556 0.1897 REMARK 3 5 1.9045 - 1.7680 0.96 2946 129 0.1631 0.2184 REMARK 3 6 1.7680 - 1.6638 0.96 2882 155 0.1545 0.2074 REMARK 3 7 1.6638 - 1.5805 0.95 2876 137 0.1547 0.1994 REMARK 3 8 1.5805 - 1.5117 0.95 2802 152 0.1534 0.2523 REMARK 3 9 1.5117 - 1.4540 0.90 2714 138 0.1630 0.2098 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) : 23.270 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 1414 REMARK 3 ANGLE : 0.703 1916 REMARK 3 CHIRALITY : 0.067 139 REMARK 3 PLANARITY : 0.005 306 REMARK 3 DIHEDRAL : 2.683 586 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 9LLR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 21-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1300055857. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAR-24 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 : SSRF REMARK 200 BEAMLINE : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9393 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27562 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 23.510 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 11.70 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 45.8600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.07500 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM FORMATE 20% PEG 3350, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 12.87100 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 6900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, 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 350 REMARK 350 BIOMOLECULE: 2 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: 6210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: F, E, D 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 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 TYR B 1 REMARK 465 GLY C 38 REMARK 465 PRO A 36 REMARK 465 LYS A 37 REMARK 465 GLY A 38 REMARK 465 TYR F 1 REMARK 465 GLY F 35 REMARK 465 ASP F 36 REMARK 465 PRO F 37 REMARK 465 GLY F 38 REMARK 465 TYR E 1 REMARK 465 PRO E 37 REMARK 465 GLY E 38 REMARK 465 PRO D 33 REMARK 465 LYS D 34 REMARK 465 GLY D 35 REMARK 465 PRO D 36 REMARK 465 LYS D 37 REMARK 465 GLY D 38 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 TYR C 1 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 TYR A 1 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 34 CB CG CD CE NZ REMARK 470 ASP E 3 CG OD1 OD2 REMARK 470 LYS E 4 CG CD CE NZ REMARK 470 LYS E 34 CG CD CE NZ REMARK 470 TYR D 1 CG CD1 CD2 CE1 CE2 CZ OH 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 C 105 O HOH A 159 2.12 REMARK 500 O HOH C 115 O HOH C 124 2.15 REMARK 500 O HOH C 102 O HOH C 127 2.17 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 O HOH C 102 O HOH A 147 2746 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH F 147 DISTANCE = 6.92 ANGSTROMS DBREF 9LLR B 1 38 PDB 9LLR 9LLR 1 38 DBREF 9LLR C 1 38 PDB 9LLR 9LLR 1 38 DBREF 9LLR A 1 38 PDB 9LLR 9LLR 1 38 DBREF 9LLR F 1 38 PDB 9LLR 9LLR 1 38 DBREF 9LLR E 1 38 PDB 9LLR 9LLR 1 38 DBREF 9LLR D 1 38 PDB 9LLR 9LLR 1 38 SEQRES 1 B 38 TYR GLY ASP LYS GLY ASP ASP GLY ASP ARG GLY ASP ASN SEQRES 2 B 38 GLY ASP LYS GLY ASP ASP GLY ASP MET GLY ASP PRO GLY SEQRES 3 B 38 ASP LYS GLY ASP ASP GLY ASP LYS GLY ASP PRO GLY SEQRES 1 C 38 TYR GLY PRO PRO GLY ASN PRO GLY PRO PRO GLY PHE PRO SEQRES 2 C 38 GLY PRO PRO GLY ASN PRO GLY PRO PRO GLY TYR PRO GLY SEQRES 3 C 38 PRO PRO GLY ASN PRO GLY GLU PRO GLY ASP PRO GLY SEQRES 1 A 38 TYR GLY PRO LYS GLY PRO LYS GLY PRO LYS GLY PRO LYS SEQRES 2 A 38 GLY PRO LYS GLY PRO LYS GLY PRO LYS GLY PRO LYS GLY SEQRES 3 A 38 PRO LYS GLY PRO LYS GLY PRO LYS GLY PRO LYS GLY SEQRES 1 F 38 TYR GLY PRO PRO GLY ASN PRO GLY PRO PRO GLY PHE PRO SEQRES 2 F 38 GLY PRO PRO GLY ASN PRO GLY PRO PRO GLY TYR PRO GLY SEQRES 3 F 38 PRO PRO GLY ASN PRO GLY GLU PRO GLY ASP PRO GLY SEQRES 1 E 38 TYR GLY ASP LYS GLY ASP ASP GLY ASP ARG GLY ASP ASN SEQRES 2 E 38 GLY ASP LYS GLY ASP ASP GLY ASP MET GLY ASP PRO GLY SEQRES 3 E 38 ASP LYS GLY ASP ASP GLY ASP LYS GLY ASP PRO GLY SEQRES 1 D 38 TYR GLY PRO LYS GLY PRO LYS GLY PRO LYS GLY PRO LYS SEQRES 2 D 38 GLY PRO LYS GLY PRO LYS GLY PRO LYS GLY PRO LYS GLY SEQRES 3 D 38 PRO LYS GLY PRO LYS GLY PRO LYS GLY PRO LYS GLY FORMUL 7 HOH *343(H2 O) CRYST1 54.534 25.742 59.077 90.00 102.46 90.00 P 1 21 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 0.018337 0.000000 0.004052 0.00000 SCALE2 0.000000 0.038847 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017335 0.00000 MASTER 287 0 0 0 0 0 0 6 1700 6 0 18 END