HEADER LIGASE 28-MAY-10 3N9B TITLE CRYSTAL STRUCTURE OF THE P. AERUGINOSA LIGD PHOSPHOESTERASE DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE ATP-DEPENDENT DNA LIGASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: PHOSPHOESTERASE DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 STRAIN: PAO1; SOURCE 5 GENE: LIGD, PA2138; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) RIL+; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS PHOSPHOESTERASE, METALLOENZYME, LIGASE, NHEJ, MANGANESE, BETA BARREL EXPDTA X-RAY DIFFRACTION AUTHOR S.SHUMAN,P.NAIR,P.SMITH REVDAT 3 21-FEB-24 3N9B 1 REMARK LINK REVDAT 2 15-SEP-10 3N9B 1 TITLE REVDAT 1 11-AUG-10 3N9B 0 JRNL AUTH P.A.NAIR,P.SMITH,S.SHUMAN JRNL TITL STRUCTURE OF BACTERIAL LIGD 3'-PHOSPHOESTERASE UNVEILS A DNA JRNL TITL 2 REPAIR SUPERFAMILY JRNL REF PROC.NATL.ACAD.SCI.USA V. 107 12822 2010 JRNL REFN ISSN 0027-8424 JRNL PMID 20616014 JRNL DOI 10.1073/PNAS.1005830107 REMARK 2 REMARK 2 RESOLUTION. 1.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6_289) 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) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.060 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 3 NUMBER OF REFLECTIONS : 23992 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.950 REMARK 3 FREE R VALUE TEST SET COUNT : 2387 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 37.4023 - 4.1348 1.00 2292 268 0.1364 0.1645 REMARK 3 2 4.1348 - 3.2826 0.99 2325 254 0.1239 0.1807 REMARK 3 3 3.2826 - 2.8678 1.00 2340 247 0.1507 0.1962 REMARK 3 4 2.8678 - 2.6057 1.00 2353 223 0.1598 0.2094 REMARK 3 5 2.6057 - 2.4189 0.99 2272 263 0.1515 0.2057 REMARK 3 6 2.4189 - 2.2763 0.94 2195 244 0.1620 0.2095 REMARK 3 7 2.2763 - 2.1624 0.70 1597 200 0.1725 0.2545 REMARK 3 8 2.1624 - 2.0682 0.94 2170 239 0.1386 0.2045 REMARK 3 9 2.0682 - 1.9886 0.92 2149 241 0.1376 0.2206 REMARK 3 10 1.9886 - 1.9200 0.82 1912 208 0.1666 0.2438 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 : 0.34 REMARK 3 B_SOL : 53.78 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.32120 REMARK 3 B22 (A**2) : -1.63510 REMARK 3 B33 (A**2) : -3.73020 REMARK 3 B12 (A**2) : -1.27090 REMARK 3 B13 (A**2) : -1.18420 REMARK 3 B23 (A**2) : 0.47540 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 : 0.010 2617 REMARK 3 ANGLE : 1.249 3556 REMARK 3 CHIRALITY : 0.100 370 REMARK 3 PLANARITY : 0.005 463 REMARK 3 DIHEDRAL : 14.969 993 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 3N9B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000059542. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-FEB-10; 20-FEB-10; 10-FEB-10 REMARK 200 TEMPERATURE (KELVIN) : 130; NULL; NULL REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y; N REMARK 200 RADIATION SOURCE : NSLS; NSLS; ROTATING ANODE REMARK 200 BEAMLINE : X12C; X25; NULL REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL; RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.19 0.99 0.73; 1.19 0.99 0.73; REMARK 200 1.54 REMARK 200 MONOCHROMATOR : SEE BEAMLINE DOCUMENTATION; REMARK 200 NULL; NULL REMARK 200 OPTICS : SEE NSLS X25 BEAMLINE REMARK 200 DESCRIPTION; SEE NSLS X12C REMARK 200 BEAMLINE DESCRIPTION; OSMIC REMARK 200 CONFOCAL MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD; IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315; ADSC QUANTUM REMARK 200 210; RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24596 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08700 REMARK 200 FOR THE DATA SET : 25.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; NULL; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZATION WAS CARRIED OUT IN REMARK 280 SITTING-DROP VAPOR-DIFFUSION SETUPS WITH 1:1 MIXTURES OF PROTEIN REMARK 280 SOLUTION CONTAINING 1.3 MM PAEPEC2 AND 2MM MNCL2 AND RESERVOIR REMARK 280 SOLUTION CONTAINING PEG 5000 MONOMETHYLETHER (MME) (20 - 30%), REMARK 280 100 MM 2-(N-MORPHOLINO) ETHANESULFONIC ACID (MES) PH 6.8 - 7.0, REMARK 280 200 MM AMMONIUM SULFATE, AND 10 MM YTTRIUM (III) CHLORIDE AT 22 REMARK 280 C. , VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 300 REMARK: PROTEIN IS MONOMER IN SOLUTION, HOWEVER, TWO PROTOMERS ARE REMARK 300 FOUND IN THE ASYMMETRIC UNIT, 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 ARG A 17 REMARK 465 GLN A 18 REMARK 465 THR A 19 REMARK 465 PRO A 20 REMARK 465 GLU A 21 REMARK 465 PRO A 22 REMARK 465 SER A 23 REMARK 465 GLY A 24 REMARK 465 ARG A 25 REMARK 465 LYS A 26 REMARK 465 PRO A 27 REMARK 465 ARG A 28 REMARK 465 LYS A 29 REMARK 465 ASP A 30 REMARK 465 SER A 31 REMARK 465 THR A 32 REMARK 465 GLY A 33 REMARK 465 GLY A 98 REMARK 465 HIS A 99 REMARK 465 TYR A 100 REMARK 465 GLY A 101 REMARK 465 THR A 186 REMARK 465 LEU A 187 REMARK 465 ARG B 17 REMARK 465 GLN B 18 REMARK 465 THR B 19 REMARK 465 PRO B 20 REMARK 465 GLU B 21 REMARK 465 PRO B 22 REMARK 465 SER B 23 REMARK 465 GLY B 24 REMARK 465 ARG B 25 REMARK 465 LYS B 26 REMARK 465 PRO B 27 REMARK 465 ARG B 28 REMARK 465 LYS B 29 REMARK 465 GLY B 98 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 GLN A 97 CG CD OE1 NE2 REMARK 470 ARG A 149 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 30 CG OD1 OD2 REMARK 470 GLN B 97 CG CD OE1 NE2 REMARK 470 HIS B 99 CG ND1 CD2 CE1 NE2 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 OE1 GLN B 80 O HOH B 241 2.00 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 OD1 ASP A 104 O HOH A 264 1655 2.12 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 VAL A 81 -165.37 -124.03 REMARK 500 ASP A 118 109.61 -37.38 REMARK 500 ASP A 118 109.61 -54.46 REMARK 500 ASP A 162 -168.33 -167.03 REMARK 500 ALA B 44 -161.93 -78.36 REMARK 500 VAL B 81 -165.48 -123.34 REMARK 500 ASP B 118 108.46 -33.98 REMARK 500 LYS B 151 21.77 -143.52 REMARK 500 ASP B 162 -168.96 -167.54 REMARK 500 GLU B 184 42.55 -103.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 YT3 A 1 Y REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 179 OD1 REMARK 620 2 HOH A 198 O 76.0 REMARK 620 3 HOH A 226 O 73.4 145.5 REMARK 620 4 HOH A 304 O 72.0 68.2 115.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 188 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SO4 A 2 O1 REMARK 620 2 HIS A 42 ND1 93.9 REMARK 620 3 HIS A 48 NE2 164.1 95.7 REMARK 620 4 ASP A 50 OD2 92.5 100.3 98.2 REMARK 620 5 HOH A 244 O 83.0 167.1 84.9 92.4 REMARK 620 6 HOH A 267 O 80.3 90.6 86.9 167.3 76.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 YT3 A 190 Y REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SO4 A 3 O4 REMARK 620 2 GLU A 135 OE1 128.1 REMARK 620 3 GLU A 135 OE2 79.9 51.6 REMARK 620 4 HOH A 215 O 136.0 74.9 124.1 REMARK 620 5 HOH A 242 O 84.1 86.0 98.9 58.1 REMARK 620 6 HOH A 300 O 147.9 70.7 102.4 69.1 126.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 YT3 A 191 Y REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SO4 A 4 O4 REMARK 620 2 ASP A 179 OD2 86.4 REMARK 620 3 GLU A 184 OE2 128.8 76.6 REMARK 620 4 GLU A 184 OE1 78.4 95.2 56.1 REMARK 620 5 HOH A 232 O 147.8 88.1 80.3 133.8 REMARK 620 6 HOH A 333 O 71.2 81.1 148.2 149.6 76.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 YT3 A 189 Y REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 124 OE2 REMARK 620 2 GLU A 124 OE1 48.2 REMARK 620 3 HOH A 303 O 68.4 59.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 188 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SO4 B 1 O3 REMARK 620 2 HIS B 42 ND1 92.2 REMARK 620 3 HIS B 48 NE2 166.2 94.8 REMARK 620 4 ASP B 50 OD2 90.2 101.0 100.1 REMARK 620 5 HOH B 208 O 82.3 90.6 85.7 166.4 REMARK 620 6 HOH B 225 O 82.2 165.8 88.2 92.1 75.7 REMARK 620 N 1 2 3 4 5 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 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 188 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE YT3 A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE YT3 A 189 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE YT3 A 190 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE YT3 A 191 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 188 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3N9D RELATED DB: PDB DBREF 3N9B A 17 187 UNP Q9I1X7 Q9I1X7_PSEAE 17 187 DBREF 3N9B B 17 187 UNP Q9I1X7 Q9I1X7_PSEAE 17 187 SEQRES 1 A 171 ARG GLN THR PRO GLU PRO SER GLY ARG LYS PRO ARG LYS SEQRES 2 A 171 ASP SER THR GLY LEU LEU ARG TYR CYS VAL GLN LYS HIS SEQRES 3 A 171 ASP ALA SER ARG LEU HIS TYR ASP PHE ARG LEU GLU LEU SEQRES 4 A 171 ASP GLY THR LEU LYS SER TRP ALA VAL PRO LYS GLY PRO SEQRES 5 A 171 CYS LEU ASP PRO ALA VAL LYS ARG LEU ALA VAL GLN VAL SEQRES 6 A 171 GLU ASP HIS PRO LEU ASP TYR ALA ASP PHE GLU GLY SER SEQRES 7 A 171 ILE PRO GLN GLY HIS TYR GLY ALA GLY ASP VAL ILE VAL SEQRES 8 A 171 TRP ASP ARG GLY ALA TRP THR PRO LEU ASP ASP PRO ARG SEQRES 9 A 171 GLU GLY LEU GLU LYS GLY HIS LEU SER PHE ALA LEU ASP SEQRES 10 A 171 GLY GLU LYS LEU SER GLY ARG TRP HIS LEU ILE ARG THR SEQRES 11 A 171 ASN LEU ARG GLY LYS GLN SER GLN TRP PHE LEU VAL LYS SEQRES 12 A 171 ALA LYS ASP GLY GLU ALA ARG SER LEU ASP ARG PHE ASP SEQRES 13 A 171 VAL LEU LYS GLU ARG PRO ASP SER VAL LEU SER GLU ARG SEQRES 14 A 171 THR LEU SEQRES 1 B 171 ARG GLN THR PRO GLU PRO SER GLY ARG LYS PRO ARG LYS SEQRES 2 B 171 ASP SER THR GLY LEU LEU ARG TYR CYS VAL GLN LYS HIS SEQRES 3 B 171 ASP ALA SER ARG LEU HIS TYR ASP PHE ARG LEU GLU LEU SEQRES 4 B 171 ASP GLY THR LEU LYS SER TRP ALA VAL PRO LYS GLY PRO SEQRES 5 B 171 CYS LEU ASP PRO ALA VAL LYS ARG LEU ALA VAL GLN VAL SEQRES 6 B 171 GLU ASP HIS PRO LEU ASP TYR ALA ASP PHE GLU GLY SER SEQRES 7 B 171 ILE PRO GLN GLY HIS TYR GLY ALA GLY ASP VAL ILE VAL SEQRES 8 B 171 TRP ASP ARG GLY ALA TRP THR PRO LEU ASP ASP PRO ARG SEQRES 9 B 171 GLU GLY LEU GLU LYS GLY HIS LEU SER PHE ALA LEU ASP SEQRES 10 B 171 GLY GLU LYS LEU SER GLY ARG TRP HIS LEU ILE ARG THR SEQRES 11 B 171 ASN LEU ARG GLY LYS GLN SER GLN TRP PHE LEU VAL LYS SEQRES 12 B 171 ALA LYS ASP GLY GLU ALA ARG SER LEU ASP ARG PHE ASP SEQRES 13 B 171 VAL LEU LYS GLU ARG PRO ASP SER VAL LEU SER GLU ARG SEQRES 14 B 171 THR LEU HET SO4 A 2 5 HET SO4 A 3 5 HET SO4 A 4 5 HET CL A 5 1 HET PEG A 6 7 HET MN A 188 1 HET YT3 A 1 1 HET YT3 A 189 1 HET YT3 A 190 1 HET YT3 A 191 1 HET SO4 B 1 5 HET MN B 188 1 HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM MN MANGANESE (II) ION HETNAM YT3 YTTRIUM (III) ION FORMUL 3 SO4 4(O4 S 2-) FORMUL 6 CL CL 1- FORMUL 7 PEG C4 H10 O3 FORMUL 8 MN 2(MN 2+) FORMUL 9 YT3 4(Y 3+) FORMUL 15 HOH *358(H2 O) HELIX 1 1 PRO A 85 PHE A 91 5 7 HELIX 2 2 ASP A 118 GLY A 126 1 9 HELIX 3 3 ASP A 172 ARG A 177 1 6 HELIX 4 4 PRO B 85 PHE B 91 5 7 HELIX 5 5 ASP B 118 GLY B 126 1 9 HELIX 6 6 ASP B 172 ARG B 177 1 6 SHEET 1 A10 GLY A 93 SER A 94 0 SHEET 2 A10 ASP A 104 PRO A 115 -1 O VAL A 105 N GLY A 93 SHEET 3 A10 HIS A 127 GLY A 134 -1 O ASP A 133 N ALA A 112 SHEET 4 A10 SER A 138 ARG A 145 -1 O TRP A 141 N PHE A 130 SHEET 5 A10 GLN A 154 LYS A 159 -1 O VAL A 158 N HIS A 142 SHEET 6 A10 ARG A 76 HIS A 84 -1 N ARG A 76 O LEU A 157 SHEET 7 A10 THR A 58 VAL A 64 -1 N ALA A 63 O VAL A 79 SHEET 8 A10 LEU A 47 LEU A 55 -1 N TYR A 49 O VAL A 64 SHEET 9 A10 LEU A 35 ASP A 43 -1 N GLN A 40 O ASP A 50 SHEET 10 A10 ASP A 104 PRO A 115 -1 O ASP A 109 N VAL A 39 SHEET 1 B10 GLY B 93 ILE B 95 0 SHEET 2 B10 GLY B 103 PRO B 115 -1 O VAL B 105 N GLY B 93 SHEET 3 B10 HIS B 127 GLY B 134 -1 O ASP B 133 N ALA B 112 SHEET 4 B10 GLY B 139 ARG B 145 -1 O TRP B 141 N PHE B 130 SHEET 5 B10 GLN B 154 LYS B 159 -1 O VAL B 158 N HIS B 142 SHEET 6 B10 ARG B 76 HIS B 84 -1 N ALA B 78 O TRP B 155 SHEET 7 B10 THR B 58 VAL B 64 -1 N ALA B 63 O VAL B 79 SHEET 8 B10 LEU B 47 LEU B 55 -1 N TYR B 49 O VAL B 64 SHEET 9 B10 ARG B 36 ASP B 43 -1 N CYS B 38 O ARG B 52 SHEET 10 B10 GLY B 103 PRO B 115 -1 O GLY B 111 N TYR B 37 LINK Y YT3 A 1 OD1 ASP A 179 1555 1555 2.44 LINK Y YT3 A 1 O HOH A 198 1555 1555 2.69 LINK Y YT3 A 1 O HOH A 226 1555 1555 2.47 LINK Y YT3 A 1 O HOH A 304 1555 1555 2.66 LINK O1 SO4 A 2 MN MN A 188 1555 1555 2.22 LINK O4 SO4 A 3 Y YT3 A 190 1555 1555 2.27 LINK O4 SO4 A 4 Y YT3 A 191 1555 1555 2.17 LINK ND1 HIS A 42 MN MN A 188 1555 1555 2.31 LINK NE2 HIS A 48 MN MN A 188 1555 1555 2.17 LINK OD2 ASP A 50 MN MN A 188 1555 1555 2.19 LINK OE2 GLU A 124 Y YT3 A 189 1555 1555 2.59 LINK OE1 GLU A 124 Y YT3 A 189 1555 1555 2.79 LINK OE1 GLU A 135 Y YT3 A 190 1555 1555 2.48 LINK OE2 GLU A 135 Y YT3 A 190 1555 1555 2.59 LINK OD2 ASP A 179 Y YT3 A 191 1555 1555 2.35 LINK OE2 GLU A 184 Y YT3 A 191 1555 1555 2.28 LINK OE1 GLU A 184 Y YT3 A 191 1555 1555 2.46 LINK MN MN A 188 O HOH A 244 1555 1555 2.49 LINK MN MN A 188 O HOH A 267 1555 1555 2.53 LINK Y YT3 A 189 O HOH A 303 1555 1555 2.54 LINK Y YT3 A 190 O HOH A 215 1555 1555 2.37 LINK Y YT3 A 190 O HOH A 242 1555 1555 2.48 LINK Y YT3 A 190 O HOH A 300 1555 1555 2.82 LINK Y YT3 A 191 O HOH A 232 1555 1555 2.42 LINK Y YT3 A 191 O HOH A 333 1555 1555 2.60 LINK O3 SO4 B 1 MN MN B 188 1555 1555 2.32 LINK ND1 HIS B 42 MN MN B 188 1555 1555 2.20 LINK NE2 HIS B 48 MN MN B 188 1555 1555 2.15 LINK OD2 ASP B 50 MN MN B 188 1555 1555 2.16 LINK MN MN B 188 O HOH B 208 1555 1555 2.66 LINK MN MN B 188 O HOH B 225 1555 1555 2.33 SITE 1 AC1 10 HIS A 42 ASP A 50 HIS A 84 MN A 188 SITE 2 AC1 10 HOH A 239 HOH A 267 HOH A 332 HOH A 364 SITE 3 AC1 10 LYS B 75 HOH B 197 SITE 1 AC2 9 GLU A 135 ARG A 177 YT3 A 190 HOH A 193 SITE 2 AC2 9 LYS B 136 ARG B 177 PRO B 178 ASP B 179 SITE 3 AC2 9 HOH B 203 SITE 1 AC3 9 LYS A 136 ARG A 177 PRO A 178 ASP A 179 SITE 2 AC3 9 GLU A 184 YT3 A 191 HOH A 333 GLU B 135 SITE 3 AC3 9 ARG B 177 SITE 1 AC4 1 ARG A 140 SITE 1 AC5 7 LYS A 161 ASP A 162 GLY A 163 ALA A 165 SITE 2 AC5 7 HOH A 292 HOH A 318 HOH B 217 SITE 1 AC6 6 SO4 A 2 HIS A 42 HIS A 48 ASP A 50 SITE 2 AC6 6 HOH A 244 HOH A 267 SITE 1 AC7 7 ASP A 117 ASP A 179 HOH A 198 HOH A 226 SITE 2 AC7 7 HOH A 294 HOH A 304 HOH A 352 SITE 1 AC8 5 ASP A 104 GLU A 124 HOH A 209 HOH A 303 SITE 2 AC8 5 HOH A 335 SITE 1 AC9 6 SO4 A 3 GLU A 135 HOH A 215 HOH A 242 SITE 2 AC9 6 HOH A 300 ASP B 179 SITE 1 BC1 6 SO4 A 4 ASP A 179 GLU A 184 HOH A 232 SITE 2 BC1 6 HOH A 333 GLU B 135 SITE 1 BC2 11 LYS A 75 HOH A 248 HIS B 42 ASP B 50 SITE 2 BC2 11 HIS B 84 TYR B 100 MN B 188 HOH B 208 SITE 3 BC2 11 HOH B 211 HOH B 225 HOH B 266 SITE 1 BC3 6 SO4 B 1 HIS B 42 HIS B 48 ASP B 50 SITE 2 BC3 6 HOH B 208 HOH B 225 CRYST1 41.583 45.550 53.384 102.32 109.43 104.59 P 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 0.024048 0.006258 0.011129 0.00000 SCALE2 0.000000 0.022685 0.007813 0.00000 SCALE3 0.000000 0.000000 0.021009 0.00000