HEADER STRUCTURAL PROTEIN 15-JUN-12 4AXY TITLE A MOLECULAR BASIS FOR THE ACTION OF THE COLLAGEN-SPECIFIC CHAPERONE TITLE 2 HSP47-SERPINH1 AND ITS STRUCTURE-SPECIFIC CLIENT RECOGNITION. COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLLAGEN-LIKE PEPTIDE; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: HSP47 BINDING COLLAGEN-LIKE PEPTIDE SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS STRUCTURAL PROTEIN, CMP EXPDTA X-RAY DIFFRACTION AUTHOR C.WIDMER,J.M.GEBAUER,E.BRUNSTEIN,S.ROSENBAUM,F.ZAUCKE,C.DROEGMUELLER, AUTHOR 2 T.LEEB,U.BAUMANN REVDAT 3 28-OCT-15 4AXY 1 SOURCE REMARK REVDAT 2 29-AUG-12 4AXY 1 JRNL REVDAT 1 15-AUG-12 4AXY 0 JRNL AUTH C.WIDMER,J.M.GEBAUER,E.BRUNSTEIN,S.ROSENBAUM,F.ZAUCKE, JRNL AUTH 2 C.DROGEMULLER,T.LEEB,U.BAUMANN JRNL TITL MOLECULAR BASIS FOR THE ACTION OF THE COLLAGEN-SPECIFIC JRNL TITL 2 CHAPERONE HSP47/SERPINH1 AND ITS STRUCTURE-SPECIFIC CLIENT JRNL TITL 3 RECOGNITION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 13243 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 22847422 JRNL DOI 10.1073/PNAS.1208072109 REMARK 2 REMARK 2 RESOLUTION. 1.24 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1051) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT 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) : 1.24 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.294 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.18 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.92 REMARK 3 NUMBER OF REFLECTIONS : 10764 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1511 REMARK 3 R VALUE (WORKING SET) : 0.1499 REMARK 3 FREE R VALUE : 0.1728 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 539 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 32.3045 - 1.9683 1.00 2682 142 0.1539 0.1734 REMARK 3 2 1.9683 - 1.5623 1.00 2547 134 0.1336 0.1501 REMARK 3 3 1.5623 - 1.3648 1.00 2517 133 0.1435 0.1871 REMARK 3 4 1.3648 - 1.2400 1.00 2479 130 0.1724 0.2111 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) : 0.12 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.18 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 355 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 68 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 : 0.011 396 REMARK 3 ANGLE : 1.444 549 REMARK 3 CHIRALITY : 0.039 41 REMARK 3 PLANARITY : 0.008 89 REMARK 3 DIHEDRAL : 7.786 176 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 4AXY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-JUN-12. REMARK 100 THE PDBE ID CODE IS EBI-52731. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.75 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD (MX-225) REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10802 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.24 REMARK 200 RESOLUTION RANGE LOW (A) : 100.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.6 REMARK 200 R MERGE (I) : 0.06 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.60 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.24 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.9 REMARK 200 R MERGE FOR SHELL (I) : 0.49 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.60 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: NULL REMARK 200 REMARK 200 REMARK: MR WAS DONE WITH PARTS OF THE STRUCTURE PUBLISHED IN THE REMARK 200 SAME ARTICLE AS THIS ENTRY. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 16.7 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.15 M AMMONIUM SULFATE, 0.05 M CITRIC REMARK 280 ACID PH 5.75 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 17.19000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 22.83500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 22.83500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.78500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 22.83500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 22.83500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 8.59500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 22.83500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 22.83500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 25.78500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 22.83500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 22.83500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 8.59500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 17.19000 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: 3610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.4 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 A2008 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2013 LIES ON A SPECIAL POSITION. REMARK 375 HOH B2008 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 O HOH A 2011 O HOH A 2012 2.02 REMARK 500 O HOH A 2019 O HOH A 2022 1.70 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 A 2001 O HOH A 2001 7555 1.92 REMARK 500 O HOH A 2011 O HOH C 2018 6545 2.03 REMARK 500 O HOH B 2004 O HOH B 2004 8554 1.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 ACETYL GROUP (ACE): THE N-TERMINUS WAS ACETYLATED TO REMARK 600 PREVENT CHARGES. REMARK 600 AMINO GROUP (NH2): THE C-TERMINUS WAS AM AMIDATED TO REMARK 600 PREVENT CHARGES. DBREF 4AXY A 0 19 PDB 4AXY 4AXY 0 19 DBREF 4AXY B 0 19 PDB 4AXY 4AXY 0 19 DBREF 4AXY C 0 19 PDB 4AXY 4AXY 0 19 SEQRES 1 A 20 ACE PRO PRO GLY PRO PRO GLY PRO THR GLY PRO ARG GLY SEQRES 2 A 20 PRO PRO GLY PRO PRO GLY NH2 SEQRES 1 B 20 ACE PRO PRO GLY PRO PRO GLY PRO THR GLY PRO ARG GLY SEQRES 2 B 20 PRO PRO GLY PRO PRO GLY NH2 SEQRES 1 C 20 ACE PRO PRO GLY PRO PRO GLY PRO THR GLY PRO ARG GLY SEQRES 2 C 20 PRO PRO GLY PRO PRO GLY NH2 HET ACE A 0 3 HET NH2 A 19 3 HET ACE B 0 3 HET NH2 B 19 3 HET ACE C 0 3 HET NH2 C 19 1 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP FORMUL 4 ACE 3(C2 H4 O) FORMUL 5 NH2 3(H2 N) FORMUL 6 HOH *68(H2 O) LINK C ACE A 0 N PRO A 1 1555 1555 1.33 LINK N NH2 A 19 C GLY A 18 1555 1555 1.33 LINK C ACE B 0 N PRO B 1 1555 1555 1.33 LINK N NH2 B 19 C GLY B 18 1555 1555 1.30 LINK C ACE C 0 N PRO C 1 1555 1555 1.33 LINK N NH2 C 19 C GLY C 18 1555 1555 1.33 CRYST1 45.670 45.670 34.380 90.00 90.00 90.00 P 43 21 2 24 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 0.021896 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021896 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029087 0.00000 HETATM 1 C ACE A 0 10.458 16.908 -1.791 1.00 33.39 C ANISOU 1 C ACE A 0 3284 4870 4534 -1902 850 619 C HETATM 2 O ACE A 0 9.472 17.343 -2.387 1.00 34.39 O ANISOU 2 O ACE A 0 3252 4527 5289 -1938 1131 54 O HETATM 3 CH3 ACE A 0 11.450 17.819 -1.131 1.00 36.61 C ANISOU 3 CH3 ACE A 0 3732 5246 4933 -2409 432 -57 C