HEADER UNKNOWN FUNCTION 19-JUN-20 6XHZ TITLE ALPHA-LYTIC PROTEASE HOMOLOG N4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: N4: HYPOTHETICAL PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES MONOMYCINI; SOURCE 3 ORGANISM_TAXID: 371720; SOURCE 4 GENE: HYPOTHETICAL PROTEIN [STREPTOMYCES MONOMYCINI].; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 ROSETTA 2(DE3)PLYSS KEYWDS PSEUDOPROTEASE, TRYPSIN-LIKE FOLD, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR C.F.NIXON,S.M.MARQUSEE,C.L.GEE REVDAT 3 18-OCT-23 6XHZ 1 REMARK REVDAT 2 10-FEB-21 6XHZ 1 JRNL REVDAT 1 20-JAN-21 6XHZ 0 JRNL AUTH C.F.NIXON,S.A.LIM,Z.R.SAILER,I.N.ZHELUDEV,C.L.GEE,B.A.KELCH, JRNL AUTH 2 M.J.HARMS,S.MARQUSEE JRNL TITL EXPLORING THE EVOLUTIONARY HISTORY OF KINETIC STABILITY IN JRNL TITL 2 THE ALPHA-LYTIC PROTEASE FAMILY. JRNL REF BIOCHEMISTRY V. 60 170 2021 JRNL REFN ISSN 0006-2960 JRNL PMID 33433210 JRNL DOI 10.1021/ACS.BIOCHEM.0C00720 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.6 REMARK 3 NUMBER OF REFLECTIONS : 39383 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 1934 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 38.6800 - 3.0100 0.97 3079 158 0.1507 0.1694 REMARK 3 2 3.0100 - 2.3900 0.98 3099 146 0.1622 0.1705 REMARK 3 3 2.3900 - 2.0800 0.99 3043 174 0.1533 0.1738 REMARK 3 4 2.0800 - 1.8900 0.99 3053 170 0.1562 0.1649 REMARK 3 5 1.8900 - 1.7600 0.99 3091 143 0.1658 0.1866 REMARK 3 6 1.7600 - 1.6500 1.00 3048 165 0.1807 0.2040 REMARK 3 7 1.6500 - 1.5700 1.00 3080 168 0.1848 0.2039 REMARK 3 8 1.5700 - 1.5000 1.00 3060 138 0.1933 0.2055 REMARK 3 9 1.5000 - 1.4500 1.00 3099 167 0.2098 0.2269 REMARK 3 10 1.4500 - 1.4000 0.96 2955 137 0.2287 0.2776 REMARK 3 11 1.4000 - 1.3500 0.78 2400 117 0.2531 0.2664 REMARK 3 12 1.3500 - 1.3100 0.65 2008 105 0.2939 0.2948 REMARK 3 13 1.3100 - 1.2800 0.50 1529 86 0.3271 0.3660 REMARK 3 14 1.2800 - 1.2500 0.30 905 60 0.4445 0.3721 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) : 0.126 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.814 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.93 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 : 0.009 1405 REMARK 3 ANGLE : 0.956 1922 REMARK 3 CHIRALITY : 0.079 220 REMARK 3 PLANARITY : 0.007 255 REMARK 3 DIHEDRAL : 17.094 494 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 6XHZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1000250114. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-MAY-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 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 : S111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39417 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 41.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.6 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 27.6 REMARK 200 DATA REDUNDANCY IN SHELL : 1.50 REMARK 200 R MERGE FOR SHELL (I) : 1.03400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.700 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: 3SGB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M LITHIUM SULFATE MONOHYDRATE, 0.1 REMARK 280 M BIS-TRIS PROPANE, PH 7.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293.15K 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 20.84750 REMARK 290 SMTRY3 2 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: 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 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 PRO A 3 REMARK 465 GLY A 196 REMARK 465 SER A 197 REMARK 465 SER A 198 REMARK 465 LEU A 199 REMARK 465 GLU A 200 REMARK 465 VAL A 201 REMARK 465 LEU A 202 REMARK 465 PHE A 203 REMARK 465 GLN A 204 REMARK 465 GLY A 205 REMARK 465 PRO A 206 REMARK 465 GLY A 207 REMARK 465 GLY A 208 REMARK 465 SER A 209 REMARK 465 SER A 210 REMARK 465 HIS A 211 REMARK 465 HIS A 212 REMARK 465 HIS A 213 REMARK 465 HIS A 214 REMARK 465 HIS A 215 REMARK 465 HIS A 216 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 527 O HOH A 575 1.98 REMARK 500 O HOH A 493 O HOH A 576 2.03 REMARK 500 O HOH A 573 O HOH A 579 2.04 REMARK 500 O HOH A 502 O HOH A 550 2.08 REMARK 500 O HOH A 427 O HOH A 457 2.18 REMARK 500 O GLY A 28 O HOH A 401 2.19 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 512 O HOH A 516 2747 1.94 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 ARG A 63 77.40 -113.71 REMARK 500 ARG A 63 77.91 -114.07 REMARK 500 PRO A 65 -160.11 -74.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 301 DBREF 6XHZ A 1 216 PDB 6XHZ 6XHZ 1 216 SEQRES 1 A 216 MET ALA PRO THR ALA VAL ARG GLY GLY ASN VAL LEU PHE SEQRES 2 A 216 SER ALA SER GLY ARG CYS THR VAL GLY PHE ASN ALA THR SEQRES 3 A 216 LYS GLY GLY THR TYR TYR ALA ILE MET GLU GLY ARG CYS SEQRES 4 A 216 VAL GLY GLY ALA ARG ASP TRP TYR ALA ASP ALA ALA ARG SEQRES 5 A 216 THR VAL HIS VAL GLY VAL THR GLU ALA VAL ARG TYR PRO SEQRES 6 A 216 GLY ASP ASP TYR ALA VAL ILE ARG TYR THR ASN THR ALA SEQRES 7 A 216 VAL SER TYR PRO GLY GLU ILE ASP LEU GLY GLY GLY ARG SEQRES 8 A 216 TYR LEU ASP VAL THR GLY ALA ALA ARG PRO VAL VAL GLY SEQRES 9 A 216 GLN SER VAL CYS LEU PRO GLY ALA THR THR GLY ARG HIS SEQRES 10 A 216 CYS GLY ARG VAL GLU ALA VAL ASN VAL SER VAL ASN HIS SEQRES 11 A 216 PRO GLU GLY THR VAL SER GLY LEU VAL ARG THR SER ALA SEQRES 12 A 216 CYS THR GLU PRO GLY THR ALA ALA GLY ARG PRO ALA VAL SEQRES 13 A 216 SER GLY SER THR ALA VAL GLY LEU ALA LEU GLY GLY GLY SEQRES 14 A 216 GLY ASN CYS ALA SER GLY GLY THR THR TYR LEU GLN PRO SEQRES 15 A 216 VAL LEU PRO ALA LEU ALA ALA PHE GLY LEU THR LEU HIS SEQRES 16 A 216 GLY SER SER LEU GLU VAL LEU PHE GLN GLY PRO GLY GLY SEQRES 17 A 216 SER SER HIS HIS HIS HIS HIS HIS HET SO4 A 301 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *184(H2 O) HELIX 1 AA1 GLY A 37 GLY A 41 1 5 HELIX 2 AA2 GLU A 146 ALA A 150 5 5 HELIX 3 AA3 VAL A 183 GLY A 191 1 9 SHEET 1 AA1 7 VAL A 11 SER A 14 0 SHEET 2 AA1 7 GLY A 17 LYS A 27 -1 O CYS A 19 N LEU A 12 SHEET 3 AA1 7 THR A 30 GLU A 36 -1 O ILE A 34 N PHE A 23 SHEET 4 AA1 7 TYR A 69 TYR A 74 -1 O ILE A 72 N ALA A 33 SHEET 5 AA1 7 HIS A 55 ARG A 63 -1 N ARG A 63 O TYR A 69 SHEET 6 AA1 7 ASP A 45 TYR A 47 -1 N TRP A 46 O VAL A 56 SHEET 7 AA1 7 VAL A 11 SER A 14 -1 N PHE A 13 O TYR A 47 SHEET 1 AA2 2 GLU A 84 GLY A 88 0 SHEET 2 AA2 2 ARG A 91 ASP A 94 -1 O ARG A 91 N LEU A 87 SHEET 1 AA3 8 GLY A 97 ALA A 98 0 SHEET 2 AA3 8 THR A 160 ALA A 165 1 O ALA A 161 N GLY A 97 SHEET 3 AA3 8 THR A 178 PRO A 182 -1 O GLN A 181 N LEU A 164 SHEET 4 AA3 8 GLY A 133 THR A 141 -1 N VAL A 139 O LEU A 180 SHEET 5 AA3 8 CYS A 118 HIS A 130 -1 N VAL A 128 O VAL A 135 SHEET 6 AA3 8 SER A 106 CYS A 108 -1 N VAL A 107 O GLY A 119 SHEET 7 AA3 8 PRO A 154 SER A 157 -1 O VAL A 156 N CYS A 108 SHEET 8 AA3 8 THR A 160 ALA A 165 -1 O VAL A 162 N ALA A 155 SSBOND 1 CYS A 19 CYS A 39 1555 1555 2.06 SSBOND 2 CYS A 108 CYS A 118 1555 1555 2.06 SSBOND 3 CYS A 144 CYS A 172 1555 1555 2.04 CISPEP 1 TYR A 64 PRO A 65 0 -6.12 SITE 1 AC1 5 GLY A 169 GLY A 170 THR A 177 HOH A 409 SITE 2 AC1 5 HOH A 497 CRYST1 39.121 41.695 51.175 90.00 98.62 90.00 P 1 21 1 2 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 0.025562 0.000000 0.003874 0.00000 SCALE2 0.000000 0.023984 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019764 0.00000