HEADER DNA BINDING PROTEIN/DNA 26-JUL-13 4LVK TITLE MOBM RELAXASE DOMAIN (MOBV; MOB_PRE) BOUND TO PLASMID PMV158 ORIT DNA TITLE 2 (22NT+3'PHOSPHATE). MN-BOUND CRYSTAL STRUCTURE AT PH 4.6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLASMID RECOMBINATION ENZYME; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RELAXASE DOMAIN OF MOBM PROTEIN; COMPND 5 SYNONYM: MOBILIZATION PROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: ACTTTAT OLIGONUCLEOTIDE; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: OLIGONUCLEOTIDE_1 MIMICKING PMV158 ORIT DNA HAIRPIN; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: ATAAAGTATAGTGTGPO OLIGONUCLEOTIDE; COMPND 14 CHAIN: C; COMPND 15 FRAGMENT: OLIGONUCLEOTIDE_2 MIMICKING PMV158 ORIT DNA HAIRPIN; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS AGALACTIAE; SOURCE 3 ORGANISM_TAXID: 1311; SOURCE 4 GENE: PRE, MOB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PQE-1; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: OLIGONUCLEOTIDES WERE OBTAINED FROM BIOMERS (ULM, SOURCE 13 GERMANY).; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 OTHER_DETAILS: OLIGONUCLEOTIDES WERE OBTAINED FROM BIOMERS (ULM, SOURCE 17 GERMANY). KEYWDS PROTEIN-DNA COMPLEX, MOB RELAXASE FAMILY, MOBV, KEYWDS 2 RELAXASE/ENDONUCLEASE, ORIT DNA, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.PLUTA,D.R.BOER,M.COLL REVDAT 3 28-FEB-24 4LVK 1 REMARK LINK REVDAT 2 18-OCT-17 4LVK 1 JRNL REVDAT 1 24-SEP-14 4LVK 0 JRNL AUTH R.PLUTA,D.R.BOER,F.LORENZO-DIAZ,S.RUSSI,H.GOMEZ, JRNL AUTH 2 C.FERNANDEZ-LOPEZ,R.PEREZ-LUQUE,M.OROZCO,M.ESPINOSA,M.COLL JRNL TITL STRUCTURAL BASIS OF A HISTIDINE-DNA NICKING/JOINING JRNL TITL 2 MECHANISM FOR GENE TRANSFER AND PROMISCUOUS SPREAD OF JRNL TITL 3 ANTIBIOTIC RESISTANCE. JRNL REF PROC. NATL. ACAD. SCI. V. 114 E6526 2017 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 28739894 JRNL DOI 10.1073/PNAS.1702971114 REMARK 2 REMARK 2 RESOLUTION. 2.37 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 2.37 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.93 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 13543 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) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 715 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) : 2.37 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.43 REMARK 3 REFLECTION IN BIN (WORKING SET) : 914 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.3360 REMARK 3 BIN FREE R VALUE SET COUNT : 51 REMARK 3 BIN FREE R VALUE : 0.4370 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1566 REMARK 3 NUCLEIC ACID ATOMS : 453 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 67 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.28000 REMARK 3 B22 (A**2) : 2.28000 REMARK 3 B33 (A**2) : -7.41000 REMARK 3 B12 (A**2) : 2.28000 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): 0.309 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.238 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.201 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.270 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2112 ; 0.012 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2926 ; 1.864 ; 1.900 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 191 ; 6.173 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 89 ;35.301 ;24.270 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 303 ;16.715 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;18.581 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 286 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1463 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 764 ; 1.920 ; 3.038 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 952 ; 2.965 ; 4.549 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1346 ; 2.674 ; 2.880 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 196 REMARK 3 ORIGIN FOR THE GROUP (A): -5.1682 42.3776 -1.7303 REMARK 3 T TENSOR REMARK 3 T11: 0.1234 T22: 0.1528 REMARK 3 T33: 0.2304 T12: -0.0375 REMARK 3 T13: 0.0456 T23: 0.0153 REMARK 3 L TENSOR REMARK 3 L11: 1.9943 L22: 1.5453 REMARK 3 L33: 4.9057 L12: 0.1199 REMARK 3 L13: 0.2688 L23: 0.1314 REMARK 3 S TENSOR REMARK 3 S11: -0.1203 S12: 0.1164 S13: -0.0170 REMARK 3 S21: 0.0094 S22: 0.0958 S23: 0.0140 REMARK 3 S31: 0.1588 S32: 0.0968 S33: 0.0246 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 7 REMARK 3 ORIGIN FOR THE GROUP (A): -16.2171 48.4559 23.9607 REMARK 3 T TENSOR REMARK 3 T11: 1.0056 T22: 0.8610 REMARK 3 T33: 0.1807 T12: 0.3373 REMARK 3 T13: 0.0701 T23: 0.0314 REMARK 3 L TENSOR REMARK 3 L11: 17.7032 L22: 11.4868 REMARK 3 L33: 4.5664 L12: 6.8828 REMARK 3 L13: 1.3439 L23: -5.5397 REMARK 3 S TENSOR REMARK 3 S11: -0.1635 S12: -0.2753 S13: 0.4563 REMARK 3 S21: 2.0911 S22: 0.5458 S23: 0.5871 REMARK 3 S31: -1.1017 S32: -0.3255 S33: -0.3823 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 12 C 27 REMARK 3 ORIGIN FOR THE GROUP (A): -6.8174 49.2334 11.3517 REMARK 3 T TENSOR REMARK 3 T11: 0.4960 T22: 0.3417 REMARK 3 T33: 0.2305 T12: -0.3045 REMARK 3 T13: 0.1233 T23: -0.0155 REMARK 3 L TENSOR REMARK 3 L11: 4.6893 L22: 1.4000 REMARK 3 L33: 0.6689 L12: 1.2476 REMARK 3 L13: 0.2372 L23: 0.8035 REMARK 3 S TENSOR REMARK 3 S11: 0.1166 S12: -0.5550 S13: 0.1725 REMARK 3 S21: 0.1857 S22: -0.0058 S23: 0.0521 REMARK 3 S31: -0.1558 S32: 0.2886 S33: -0.1108 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4LVK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1000081139. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97300 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13543 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.370 REMARK 200 RESOLUTION RANGE LOW (A) : 37.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 8.400 REMARK 200 R MERGE (I) : 0.10700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.37 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% PEG 4000, 0.2M SODIUM CHLORIDE, REMARK 280 0.1M SODIUM ACETATE PH4.6., VAPOR DIFFUSION + SEEDING, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.55333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 61.10667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 45.83000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 76.38333 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 15.27667 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 30.55333 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 61.10667 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 76.38333 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 45.83000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 15.27667 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: 5120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.0 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 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 PHE A 27 REMARK 465 GLU A 28 REMARK 465 THR A 29 REMARK 465 HIS A 30 REMARK 465 ALA A 197 REMARK 465 ASP A 198 REMARK 465 MET A 199 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 DT C 27 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DT C 27 N1 C2 O2 N3 C4 O4 C5 REMARK 470 DT C 27 C7 C6 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 NH2 ARG A 194 NH2 ARG A 194 10664 1.63 REMARK 500 REMARK 500 REMARK: NULL 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 DT B 3 N1 DT B 3 C2 0.053 REMARK 500 DT B 3 N3 DT B 3 C4 -0.061 REMARK 500 DT B 3 C4 DT B 3 C5 0.062 REMARK 500 DT B 3 C5 DT B 3 C6 0.054 REMARK 500 DT B 4 N1 DT B 4 C2 0.066 REMARK 500 DT B 4 N3 DT B 4 C4 -0.052 REMARK 500 DT B 4 C4 DT B 4 C5 0.057 REMARK 500 DT B 4 C5 DT B 4 C6 0.059 REMARK 500 DT B 5 N3 DT B 5 C4 -0.052 REMARK 500 DT B 5 C5 DT B 5 C6 0.052 REMARK 500 DT B 7 C4 DT B 7 C5 0.057 REMARK 500 DT B 7 C5 DT B 7 C6 0.061 REMARK 500 DT C 13 N1 DT C 13 C2 0.056 REMARK 500 DT C 13 C5 DT C 13 C6 0.056 REMARK 500 DT C 18 N1 DT C 18 C2 0.071 REMARK 500 DT C 18 N3 DT C 18 C4 -0.050 REMARK 500 DT C 18 C5 DT C 18 C6 0.054 REMARK 500 DT C 20 C5 DT C 20 C6 0.045 REMARK 500 DT C 25 N3 DT C 25 C4 -0.055 REMARK 500 DT C 25 C5 DT C 25 C6 0.059 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 DT B 3 N1 - C2 - N3 ANGL. DEV. = 7.5 DEGREES REMARK 500 DT B 3 C2 - N3 - C4 ANGL. DEV. = -7.2 DEGREES REMARK 500 DT B 3 N3 - C4 - C5 ANGL. DEV. = 5.3 DEGREES REMARK 500 DT B 3 C5 - C6 - N1 ANGL. DEV. = -4.2 DEGREES REMARK 500 DT B 3 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 DT B 3 C4 - C5 - C7 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT B 4 N1 - C2 - N3 ANGL. DEV. = 7.3 DEGREES REMARK 500 DT B 4 C2 - N3 - C4 ANGL. DEV. = -6.9 DEGREES REMARK 500 DT B 4 N3 - C4 - C5 ANGL. DEV. = 4.6 DEGREES REMARK 500 DT B 4 C5 - C6 - N1 ANGL. DEV. = -4.1 DEGREES REMARK 500 DT B 4 N3 - C2 - O2 ANGL. DEV. = -5.5 DEGREES REMARK 500 DT B 5 O5' - P - OP2 ANGL. DEV. = -5.8 DEGREES REMARK 500 DT B 5 O5' - C5' - C4' ANGL. DEV. = -5.9 DEGREES REMARK 500 DT B 5 N1 - C2 - N3 ANGL. DEV. = 8.4 DEGREES REMARK 500 DT B 5 C2 - N3 - C4 ANGL. DEV. = -9.3 DEGREES REMARK 500 DT B 5 N3 - C4 - C5 ANGL. DEV. = 7.1 DEGREES REMARK 500 DT B 5 C5 - C6 - N1 ANGL. DEV. = -4.5 DEGREES REMARK 500 DT B 5 N1 - C2 - O2 ANGL. DEV. = -5.4 DEGREES REMARK 500 DT B 5 C5 - C4 - O4 ANGL. DEV. = -6.1 DEGREES REMARK 500 DT B 7 O5' - P - OP1 ANGL. DEV. = -7.2 DEGREES REMARK 500 DT B 7 C1' - O4' - C4' ANGL. DEV. = 4.4 DEGREES REMARK 500 DT B 7 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 DT B 7 C6 - N1 - C2 ANGL. DEV. = -3.0 DEGREES REMARK 500 DT B 7 N1 - C2 - N3 ANGL. DEV. = 8.9 DEGREES REMARK 500 DT B 7 C2 - N3 - C4 ANGL. DEV. = -7.3 DEGREES REMARK 500 DT B 7 N3 - C4 - C5 ANGL. DEV. = 4.3 DEGREES REMARK 500 DT B 7 N1 - C2 - O2 ANGL. DEV. = -5.7 DEGREES REMARK 500 DT C 13 C4' - C3' - C2' ANGL. DEV. = 5.8 DEGREES REMARK 500 DT C 13 N1 - C2 - N3 ANGL. DEV. = 6.9 DEGREES REMARK 500 DT C 13 C2 - N3 - C4 ANGL. DEV. = -6.5 DEGREES REMARK 500 DT C 13 N3 - C4 - C5 ANGL. DEV. = 4.7 DEGREES REMARK 500 DT C 13 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 DT C 18 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 DT C 18 C6 - N1 - C2 ANGL. DEV. = -3.4 DEGREES REMARK 500 DT C 18 N1 - C2 - N3 ANGL. DEV. = 8.2 DEGREES REMARK 500 DT C 18 C2 - N3 - C4 ANGL. DEV. = -6.7 DEGREES REMARK 500 DT C 18 N3 - C4 - C5 ANGL. DEV. = 4.7 DEGREES REMARK 500 DT C 18 N3 - C2 - O2 ANGL. DEV. = -7.7 DEGREES REMARK 500 DT C 20 N1 - C2 - N3 ANGL. DEV. = 4.8 DEGREES REMARK 500 DT C 20 C2 - N3 - C4 ANGL. DEV. = -6.2 DEGREES REMARK 500 DT C 20 N3 - C4 - C5 ANGL. DEV. = 5.4 DEGREES REMARK 500 DT C 20 C5 - C6 - N1 ANGL. DEV. = -3.9 DEGREES REMARK 500 DT C 20 C5 - C4 - O4 ANGL. DEV. = -5.8 DEGREES REMARK 500 DT C 23 N1 - C2 - N3 ANGL. DEV. = 5.8 DEGREES REMARK 500 DT C 23 C2 - N3 - C4 ANGL. DEV. = -6.5 DEGREES REMARK 500 DT C 23 N3 - C4 - C5 ANGL. DEV. = 5.0 DEGREES REMARK 500 DT C 23 C5 - C6 - N1 ANGL. DEV. = -3.8 DEGREES REMARK 500 DT C 23 N3 - C2 - O2 ANGL. DEV. = -4.0 DEGREES REMARK 500 DT C 25 O4' - C1' - N1 ANGL. DEV. = 8.2 DEGREES REMARK 500 DT C 25 C6 - N1 - C2 ANGL. DEV. = -3.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 54 ANGLE DEVIATIONS. 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 ASP A 48 41.91 -102.41 REMARK 500 SER A 87 -149.51 -154.08 REMARK 500 ALA A 123 88.86 -161.73 REMARK 500 GLU A 129 -159.97 -109.14 REMARK 500 SER A 147 100.41 -161.83 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 MN A 201 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 126 ND1 REMARK 620 2 GLU A 129 OE2 98.3 REMARK 620 3 HIS A 133 NE2 111.7 95.1 REMARK 620 4 HIS A 135 NE2 89.6 168.0 90.2 REMARK 620 5 DG C 26 O3' 161.4 78.5 87.0 91.1 REMARK 620 6 DT C 27 OP1 100.8 81.6 147.5 88.2 60.7 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 MN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 101 DBREF 4LVK A 2 199 UNP P13925 PRE_STRAG 2 199 DBREF 4LVK B 1 7 PDB 4LVK 4LVK 1 7 DBREF 4LVK C 12 27 PDB 4LVK 4LVK 12 27 SEQRES 1 A 198 SER TYR MET VAL ALA ARG MET GLN LYS MET LYS ALA GLY SEQRES 2 A 198 ASN LEU GLY GLY ALA PHE LYS HIS ASN GLU ARG VAL PHE SEQRES 3 A 198 GLU THR HIS SER ASN LYS ASP ILE ASN PRO SER ARG SER SEQRES 4 A 198 HIS LEU ASN TYR GLU LEU THR ASP ARG ASP ARG SER VAL SEQRES 5 A 198 SER TYR GLU LYS GLN ILE LYS ASP TYR VAL ASN GLU ASN SEQRES 6 A 198 LYS VAL SER ASN ARG ALA ILE ARG LYS ASP ALA VAL LEU SEQRES 7 A 198 CYS ASP GLU TRP ILE ILE THR SER ASP LYS ASP PHE PHE SEQRES 8 A 198 GLU LYS LEU ASP GLU GLU GLN THR ARG THR PHE PHE GLU SEQRES 9 A 198 THR ALA LYS ASN TYR PHE ALA GLU ASN TYR GLY GLU SER SEQRES 10 A 198 ASN ILE ALA TYR ALA SER VAL HIS LEU ASP GLU SER THR SEQRES 11 A 198 PRO HIS MET HIS MET GLY VAL VAL PRO PHE GLU ASN GLY SEQRES 12 A 198 LYS LEU SER SER LYS ALA MET PHE ASP ARG GLU GLU LEU SEQRES 13 A 198 LYS HIS ILE GLN GLU ASP LEU PRO ARG TYR MET SER ASP SEQRES 14 A 198 HIS GLY PHE GLU LEU GLU ARG GLY LYS LEU ASN SER GLU SEQRES 15 A 198 ALA LYS HIS LYS THR VAL ALA GLU PHE LYS ARG ALA MET SEQRES 16 A 198 ALA ASP MET SEQRES 1 B 7 DA DC DT DT DT DA DT SEQRES 1 C 16 DA DT DA DA DA DG DT DA DT DA DG DT DG SEQRES 2 C 16 DT DG DT HET MN A 201 1 HET NA B 101 1 HETNAM MN MANGANESE (II) ION HETNAM NA SODIUM ION FORMUL 4 MN MN 2+ FORMUL 5 NA NA 1+ FORMUL 6 HOH *67(H2 O) HELIX 1 1 LYS A 12 GLU A 24 1 13 HELIX 2 2 ASN A 36 ASN A 43 5 8 HELIX 3 3 SER A 54 LYS A 67 1 14 HELIX 4 4 ASP A 88 LYS A 94 1 7 HELIX 5 5 ASP A 96 GLY A 116 1 21 HELIX 6 6 SER A 147 PHE A 152 1 6 HELIX 7 7 ASP A 153 ASP A 170 1 18 HELIX 8 8 THR A 188 MET A 196 1 9 SHEET 1 A 5 VAL A 5 MET A 11 0 SHEET 2 A 5 CYS A 80 THR A 86 -1 O ILE A 84 N ARG A 7 SHEET 3 A 5 HIS A 133 VAL A 138 -1 O MET A 136 N TRP A 83 SHEET 4 A 5 ILE A 120 HIS A 126 -1 N SER A 124 O HIS A 135 SHEET 5 A 5 TYR A 44 GLU A 45 -1 N TYR A 44 O VAL A 125 SHEET 1 B 2 PHE A 141 GLU A 142 0 SHEET 2 B 2 LYS A 145 LEU A 146 -1 O LYS A 145 N GLU A 142 LINK ND1 HIS A 126 MN MN A 201 1555 1555 2.05 LINK OE2 GLU A 129 MN MN A 201 1555 1555 1.94 LINK NE2 HIS A 133 MN MN A 201 1555 1555 2.03 LINK NE2 HIS A 135 MN MN A 201 1555 1555 2.07 LINK MN MN A 201 O3' DG C 26 1555 1555 2.64 LINK MN MN A 201 OP1 DT C 27 1555 1555 2.18 LINK OP2 DT B 3 NA NA B 101 1555 1555 2.39 SITE 1 AC1 6 HIS A 126 GLU A 129 HIS A 133 HIS A 135 SITE 2 AC1 6 DG C 26 DT C 27 SITE 1 AC2 1 DT B 3 CRYST1 112.743 112.743 91.660 90.00 90.00 120.00 P 61 2 2 12 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 0.008870 0.005121 0.000000 0.00000 SCALE2 0.000000 0.010242 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010910 0.00000