HEADER HYDROLASE 14-MAY-19 6RPV TITLE EXTREMELY STABLE MONOMERIC VARIANT OF HUMAN CYSTATIN C WITH SINGLE TITLE 2 AMINO ACID SUBSTITUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYSTATIN-C; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYSTATIN-3,GAMMA-TRACE,NEUROENDOCRINE BASIC POLYPEPTIDE, COMPND 5 POST-GAMMA-GLOBULIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CST3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN STRUCTURE, HUMAN CYSTATIN C, HCC V57G MUTATION, HYDROLASE EXPDTA SOLUTION NMR; SOLUTION SCATTERING NUMMDL 20 AUTHOR I.ZHUKOV,S.RODZIEWICZ-MOTOWIDLO,M.MASZOTA-ZIELENIAK,P.JURCZAK,M.KOZAK REVDAT 4 14-JUN-23 6RPV 1 REMARK REVDAT 3 29-JAN-20 6RPV 1 JRNL REVDAT 2 21-AUG-19 6RPV 1 AUTHOR REMARK REVDAT 1 31-JUL-19 6RPV 0 JRNL AUTH M.MASZOTA-ZIELENIAK,P.JURCZAK,M.ORLIKOWSKA,I.ZHUKOV,D.BOREK, JRNL AUTH 2 Z.OTWINOWSKI,P.SKOWRON,Z.PIETRALIK,M.KOZAK,A.SZYMANSKA, JRNL AUTH 3 S.RODZIEWICZ-MOTOWIDLO JRNL TITL NMR AND CRYSTALLOGRAPHIC STRUCTURAL STUDIES OF THE EXTREMELY JRNL TITL 2 STABLE MONOMERIC VARIANT OF HUMAN CYSTATIN C WITH SINGLE JRNL TITL 3 AMINO ACID SUBSTITUTION. JRNL REF FEBS J. V. 287 361 2020 JRNL REFN ISSN 1742-464X JRNL PMID 31330077 JRNL DOI 10.1111/FEBS.15010 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH, YASARA REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (XPLOR REMARK 3 -NIH), KRIEGER E. (YASARA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6RPV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1292102374. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : 1 PA REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-99% 15N] HCC V57G, 90% REMARK 210 H2O/10% D2O; 0.5 MM [U-99% 13C; REMARK 210 U-99% 15N] HCC V57G, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HNCA; 3D HN(CO)CA; REMARK 210 3D CBCA(CO)NH; 3D HBHA(CO)NH; 3D REMARK 210 HCCH-TOCSY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : DDR2 REMARK 210 SPECTROMETER MANUFACTURER : AGILENT REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, SPARKY, CS-ROSETTA, REMARK 210 CYANA REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 265 REMARK 265 EXPERIMENTAL DETAILS 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 4 GLU A 20 CB GLU A 20 CG -0.117 REMARK 500 10 GLU A 20 CB GLU A 20 CG -0.116 REMARK 500 13 VAL A 31 CB VAL A 31 CG2 -0.127 REMARK 500 14 GLU A 20 CB GLU A 20 CG -0.115 REMARK 500 14 VAL A 31 CB VAL A 31 CG2 -0.132 REMARK 500 15 VAL A 31 CB VAL A 31 CG2 -0.131 REMARK 500 17 GLU A 20 CB GLU A 20 CG -0.152 REMARK 500 18 GLU A 20 CB GLU A 20 CG -0.123 REMARK 500 20 VAL A 31 CB VAL A 31 CG2 -0.131 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 PRO A 105 C - N - CA ANGL. DEV. = -12.5 DEGREES REMARK 500 1 PRO A 105 C - N - CD ANGL. DEV. = 12.7 DEGREES REMARK 500 2 PRO A 105 C - N - CA ANGL. DEV. = -12.8 DEGREES REMARK 500 2 PRO A 105 C - N - CD ANGL. DEV. = 12.7 DEGREES REMARK 500 3 PRO A 105 C - N - CA ANGL. DEV. = -13.0 DEGREES REMARK 500 3 PRO A 105 C - N - CD ANGL. DEV. = 13.1 DEGREES REMARK 500 4 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 PRO A 105 C - N - CA ANGL. DEV. = -12.5 DEGREES REMARK 500 4 PRO A 105 C - N - CD ANGL. DEV. = 12.7 DEGREES REMARK 500 5 PRO A 105 C - N - CA ANGL. DEV. = -12.8 DEGREES REMARK 500 5 PRO A 105 C - N - CD ANGL. DEV. = 12.9 DEGREES REMARK 500 6 PRO A 105 C - N - CA ANGL. DEV. = -12.6 DEGREES REMARK 500 6 PRO A 105 C - N - CD ANGL. DEV. = 12.6 DEGREES REMARK 500 7 PRO A 105 C - N - CA ANGL. DEV. = -12.6 DEGREES REMARK 500 7 PRO A 105 C - N - CD ANGL. DEV. = 12.7 DEGREES REMARK 500 8 PRO A 105 C - N - CA ANGL. DEV. = -12.5 DEGREES REMARK 500 9 PRO A 105 C - N - CA ANGL. DEV. = -12.9 DEGREES REMARK 500 9 PRO A 105 C - N - CD ANGL. DEV. = 12.8 DEGREES REMARK 500 10 PRO A 105 C - N - CA ANGL. DEV. = -12.8 DEGREES REMARK 500 10 PRO A 105 C - N - CD ANGL. DEV. = 12.7 DEGREES REMARK 500 11 ARG A 24 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 11 PRO A 105 C - N - CA ANGL. DEV. = -12.8 DEGREES REMARK 500 11 PRO A 105 C - N - CD ANGL. DEV. = 13.1 DEGREES REMARK 500 12 PRO A 105 C - N - CA ANGL. DEV. = -12.7 DEGREES REMARK 500 12 PRO A 105 C - N - CD ANGL. DEV. = 12.7 DEGREES REMARK 500 13 PRO A 105 C - N - CA ANGL. DEV. = -12.8 DEGREES REMARK 500 13 PRO A 105 C - N - CD ANGL. DEV. = 12.9 DEGREES REMARK 500 14 ARG A 70 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 14 PRO A 105 C - N - CA ANGL. DEV. = -12.6 DEGREES REMARK 500 14 PRO A 105 C - N - CD ANGL. DEV. = 12.6 DEGREES REMARK 500 15 PRO A 105 C - N - CA ANGL. DEV. = -12.8 DEGREES REMARK 500 15 PRO A 105 C - N - CD ANGL. DEV. = 13.0 DEGREES REMARK 500 16 CYS A 97 CA - CB - SG ANGL. DEV. = 6.6 DEGREES REMARK 500 16 PRO A 105 C - N - CA ANGL. DEV. = -12.7 DEGREES REMARK 500 16 PRO A 105 C - N - CD ANGL. DEV. = 12.8 DEGREES REMARK 500 17 PRO A 105 C - N - CA ANGL. DEV. = -12.8 DEGREES REMARK 500 17 PRO A 105 C - N - CD ANGL. DEV. = 12.8 DEGREES REMARK 500 18 PRO A 105 C - N - CA ANGL. DEV. = -12.6 DEGREES REMARK 500 18 PRO A 105 C - N - CD ANGL. DEV. = 12.6 DEGREES REMARK 500 19 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 19 PRO A 105 C - N - CA ANGL. DEV. = -12.5 DEGREES REMARK 500 19 PRO A 105 C - N - CD ANGL. DEV. = 12.7 DEGREES REMARK 500 20 ARG A 70 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 20 PRO A 105 C - N - CA ANGL. DEV. = -12.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 1 VAL A 10 -71.37 -136.75 REMARK 500 1 LEU A 91 90.69 -68.63 REMARK 500 2 ASN A 39 55.45 -93.70 REMARK 500 3 SER A 2 69.51 38.60 REMARK 500 3 ASN A 79 33.84 -95.74 REMARK 500 4 VAL A 10 -37.74 69.03 REMARK 500 4 ASN A 39 57.34 -93.64 REMARK 500 4 LEU A 91 92.85 -64.74 REMARK 500 7 LYS A 5 58.75 -152.85 REMARK 500 7 ASN A 79 40.55 -140.55 REMARK 500 7 LEU A 91 98.48 -69.82 REMARK 500 8 LEU A 9 63.60 -101.56 REMARK 500 8 ASN A 39 52.53 -97.98 REMARK 500 8 ALA A 46 102.21 -56.41 REMARK 500 9 ASN A 39 53.67 -98.64 REMARK 500 9 LEU A 91 91.41 -62.17 REMARK 500 10 ASN A 39 54.87 -91.99 REMARK 500 10 LEU A 91 90.86 -67.32 REMARK 500 11 ASN A 39 53.72 -92.05 REMARK 500 13 ASN A 39 56.72 -90.03 REMARK 500 14 ASN A 39 51.96 -95.55 REMARK 500 14 PRO A 78 28.38 -76.60 REMARK 500 15 LEU A 9 60.82 -101.04 REMARK 500 15 ASN A 39 51.42 -101.32 REMARK 500 18 SER A 2 63.36 37.25 REMARK 500 19 ASN A 39 54.97 -90.11 REMARK 500 20 ASN A 39 55.43 -99.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34399 RELATED DB: BMRB REMARK 900 EXTREMELY STABLE MONOMERIC VARIANT OF HUMAN CYSTATIN C WITH SINGLE REMARK 900 AMINO ACID SUBSTITUTION DBREF 6RPV A 1 120 UNP P01034 CYTC_HUMAN 27 146 SEQADV 6RPV GLY A 57 UNP P01034 VAL 83 ENGINEERED MUTATION SEQRES 1 A 120 SER SER PRO GLY LYS PRO PRO ARG LEU VAL GLY GLY PRO SEQRES 2 A 120 MET ASP ALA SER VAL GLU GLU GLU GLY VAL ARG ARG ALA SEQRES 3 A 120 LEU ASP PHE ALA VAL GLY GLU TYR ASN LYS ALA SER ASN SEQRES 4 A 120 ASP MET TYR HIS SER ARG ALA LEU GLN VAL VAL ARG ALA SEQRES 5 A 120 ARG LYS GLN ILE GLY ALA GLY VAL ASN TYR PHE LEU ASP SEQRES 6 A 120 VAL GLU LEU GLY ARG THR THR CYS THR LYS THR GLN PRO SEQRES 7 A 120 ASN LEU ASP ASN CYS PRO PHE HIS ASP GLN PRO HIS LEU SEQRES 8 A 120 LYS ARG LYS ALA PHE CYS SER PHE GLN ILE TYR ALA VAL SEQRES 9 A 120 PRO TRP GLN GLY THR MET THR LEU SER LYS SER THR CYS SEQRES 10 A 120 GLN ASP ALA HELIX 1 AA1 GLU A 20 ASN A 35 1 16 HELIX 2 AA2 ASP A 81 LEU A 91 1 11 HELIX 3 AA3 PRO A 105 GLY A 108 5 4 SHEET 1 AA1 5 GLY A 12 ASP A 15 0 SHEET 2 AA1 5 SER A 44 ILE A 56 -1 O LYS A 54 N MET A 14 SHEET 3 AA1 5 VAL A 60 ARG A 70 -1 O PHE A 63 N ARG A 53 SHEET 4 AA1 5 ALA A 95 VAL A 104 -1 O ALA A 103 N VAL A 60 SHEET 5 AA1 5 THR A 109 THR A 116 -1 O THR A 111 N TYR A 102 SSBOND 1 CYS A 73 CYS A 83 1555 1555 2.02 SSBOND 2 CYS A 97 CYS A 117 1555 1555 2.03 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1