HEADER HYDROLASE 07-SEP-21 7PNJ TITLE HUMAN ANGIOGENIN QUARDRUPLE MUTANT-S28AT36AS37AS87A COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANGIOGENIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RIBONUCLEASE 5,RNASE 5; COMPND 5 EC: 3.1.27.-; 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: ANG, RNASE5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RNASE5, ANGIOGENESIS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR O.S.E.PAPAIOANNOU,D.D.LEONIDAS REVDAT 5 09-OCT-24 7PNJ 1 REMARK REVDAT 4 07-FEB-24 7PNJ 1 REMARK REVDAT 3 14-JUN-23 7PNJ 1 JRNL REVDAT 2 31-MAY-23 7PNJ 1 JRNL REVDAT 1 29-SEP-21 7PNJ 0 JRNL AUTH O.S.E.PAPAIOANNOU,A.C.TSIKA,M.ROVOLI,G.E.PAPADOPOULOS, JRNL AUTH 2 G.KONTOPIDIS,G.A.SPYROULIAS,D.D.LEONIDAS JRNL TITL STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF THE HUMAN JRNL TITL 2 ANGIOGENIN-PROLIFERATING CELL NUCLEAR ANTIGEN INTERACTION. JRNL REF BIOCHEMISTRY V. 62 1706 2023 JRNL REFN ISSN 0006-2960 JRNL PMID 37218877 JRNL DOI 10.1021/ACS.BIOCHEM.3C00158 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 2359 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.252 REMARK 3 R VALUE (WORKING SET) : 0.250 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 257 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.18 REMARK 3 REFLECTION IN BIN (WORKING SET) : 161 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3590 REMARK 3 BIN FREE R VALUE SET COUNT : 18 REMARK 3 BIN FREE R VALUE : 0.4590 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 961 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 15 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.81000 REMARK 3 B22 (A**2) : -1.89000 REMARK 3 B33 (A**2) : 2.69000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.574 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.445 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 26.705 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.880 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.840 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 999 ; 0.003 ; 0.017 REMARK 3 BOND LENGTHS OTHERS (A): 917 ; 0.001 ; 0.019 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1351 ; 1.022 ; 1.828 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2103 ; 0.871 ; 2.583 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 119 ; 5.850 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 64 ;26.894 ;20.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 165 ;12.751 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;11.519 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 136 ; 0.057 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1157 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 259 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.00 REMARK 3 ION PROBE RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 7PNJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1292118018. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAY-19 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 : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2632 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 68.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.31 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLREP REMARK 200 STARTING MODEL: 1B1I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM CITRATE PH 5.6, 25% REMARK 280 (W/V) PEG 4000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 21 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,-Z+1/2 REMARK 290 4555 -X+1/2,-Y,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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 17.28400 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.33000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 17.28400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 34.33000 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: MONOMERIC 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 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 312 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 314 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 GLN A 1 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 PRO A 18 -70.13 -59.19 REMARK 500 GLN A 19 -103.47 97.02 REMARK 500 ARG A 21 35.92 -140.18 REMARK 500 ASP A 22 -164.78 -111.03 REMARK 500 ALA A 37 79.14 -170.00 REMARK 500 ASN A 61 27.98 -140.46 REMARK 500 ARG A 66 -100.53 22.25 REMARK 500 ASP A 116 94.26 -65.60 REMARK 500 PHE A 120 -75.17 -74.77 REMARK 500 REMARK 500 REMARK: NULL DBREF 7PNJ A 1 121 UNP P03950 ANGI_HUMAN 25 145 SEQADV 7PNJ ALA A 28 UNP P03950 SER 52 ENGINEERED MUTATION SEQADV 7PNJ ALA A 36 UNP P03950 THR 60 ENGINEERED MUTATION SEQADV 7PNJ ALA A 37 UNP P03950 SER 61 ENGINEERED MUTATION SEQADV 7PNJ ALA A 87 UNP P03950 SER 111 ENGINEERED MUTATION SEQRES 1 A 121 GLN ASP ASN SER ARG TYR THR HIS PHE LEU THR GLN HIS SEQRES 2 A 121 TYR ASP ALA LYS PRO GLN GLY ARG ASP ASP ARG TYR CYS SEQRES 3 A 121 GLU ALA ILE MET ARG ARG ARG GLY LEU ALA ALA PRO CYS SEQRES 4 A 121 LYS ASP ILE ASN THR PHE ILE HIS GLY ASN LYS ARG SER SEQRES 5 A 121 ILE LYS ALA ILE CYS GLU ASN LYS ASN GLY ASN PRO HIS SEQRES 6 A 121 ARG GLU ASN LEU ARG ILE SER LYS SER SER PHE GLN VAL SEQRES 7 A 121 THR THR CYS LYS LEU HIS GLY GLY ALA PRO TRP PRO PRO SEQRES 8 A 121 CYS GLN TYR ARG ALA THR ALA GLY PHE ARG ASN VAL VAL SEQRES 9 A 121 VAL ALA CYS GLU ASN GLY LEU PRO VAL HIS LEU ASP GLN SEQRES 10 A 121 SER ILE PHE ARG HET CIT A 201 13 HETNAM CIT CITRIC ACID FORMUL 2 CIT C6 H8 O7 FORMUL 3 HOH *15(H2 O) HELIX 1 AA1 ASN A 3 TYR A 14 1 12 HELIX 2 AA2 ASP A 22 ARG A 33 1 12 HELIX 3 AA3 ASN A 49 ALA A 55 1 7 HELIX 4 AA4 GLN A 117 PHE A 120 5 4 SHEET 1 AA1 3 ILE A 42 HIS A 47 0 SHEET 2 AA1 3 PHE A 76 HIS A 84 -1 O CYS A 81 N ASN A 43 SHEET 3 AA1 3 GLN A 93 ARG A 101 -1 O GLN A 93 N HIS A 84 SHEET 1 AA2 4 GLY A 62 HIS A 65 0 SHEET 2 AA2 4 LEU A 69 SER A 72 -1 O ILE A 71 N ASN A 63 SHEET 3 AA2 4 VAL A 104 GLU A 108 -1 O VAL A 105 N ARG A 70 SHEET 4 AA2 4 LEU A 111 LEU A 115 -1 O LEU A 111 N GLU A 108 SSBOND 1 CYS A 26 CYS A 81 1555 1555 2.03 SSBOND 2 CYS A 39 CYS A 92 1555 1555 2.03 SSBOND 3 CYS A 57 CYS A 107 1555 1555 2.04 CISPEP 1 ALA A 37 PRO A 38 0 -1.81 CISPEP 2 PRO A 90 PRO A 91 0 -0.01 CRYST1 34.568 55.052 68.660 90.00 90.00 90.00 P 21 2 21 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 0.028928 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018165 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014565 0.00000