HEADER OXIDOREDUCTASE 28-AUG-14 4W9Z TITLE CRYSTAL STRUCTURE OF THE PERIPLASMIC DOMAIN OF SUBUNIT II OF TITLE 2 CYTOCHROME OXIDASE (COXB) OF BRADYRHIZOBIUM JAPONICUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C OXIDASE SUBUNIT 2; COMPND 3 CHAIN: A; COMPND 4 EC: 1.9.3.1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BRADYRHIZOBIUM DIAZOEFFICIENS; SOURCE 3 ORGANISM_TAXID: 224911; SOURCE 4 STRAIN: JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110; SOURCE 5 GENE: COXB, BLR1170; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11A-COXBPD KEYWDS OXIDOREDUCTASE, CUA, RESPIRATION EXPDTA X-RAY DIFFRACTION AUTHOR N.QUADE,H.K.ABICHT,H.HENNECKE,R.GLOCKSHUBER REVDAT 2 10-JAN-24 4W9Z 1 REMARK REVDAT 1 09-SEP-15 4W9Z 0 JRNL AUTH N.QUADE,H.K.ABICHT,H.HENNECKE,R.GLOCKSHUBER JRNL TITL CRYSTAL STRUCTURE OF THE PERIPLASMIC DOMAIN OF SUBUNIT II OF JRNL TITL 2 CYTOCHROME OXIDASE (COXB) OF BRADYRHIZOBIUM JAPONICUM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.12 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 34089 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) : 0.110 REMARK 3 R VALUE (WORKING SET) : 0.109 REMARK 3 FREE R VALUE : 0.134 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1795 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) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2512 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.44 REMARK 3 BIN R VALUE (WORKING SET) : 0.1210 REMARK 3 BIN FREE R VALUE SET COUNT : 133 REMARK 3 BIN FREE R VALUE : 0.1330 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1091 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 256 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.28000 REMARK 3 B22 (A**2) : 0.46000 REMARK 3 B33 (A**2) : -0.16000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.08000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.036 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.036 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.019 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.955 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.980 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.975 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1155 ; 0.026 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 1117 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1570 ; 2.270 ; 1.940 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2586 ; 1.238 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 148 ; 8.812 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 50 ;35.294 ;24.600 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 203 ;13.508 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;14.590 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 170 ; 0.131 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1296 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 264 ; 0.004 ; 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): 563 ; 2.457 ; 1.110 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 562 ; 2.409 ; 1.103 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 704 ; 3.219 ; 1.673 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): 2272 ; 6.327 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 46 ;37.673 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2449 ;15.054 ; 5.000 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 : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4W9Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000203435. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-AUG-14 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA 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 : 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, XSCALE REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35883 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.1300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.24700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.250 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: 4TXV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M POTASSIUM BROMIDE, 0.1M TRIS PH REMARK 280 7.5, 10% PEG1000, 10% PEG8000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K 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 19.30600 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 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 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 SER A 265 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 515 O HOH A 631 0.20 REMARK 500 O HOH A 516 O HOH A 599 0.25 REMARK 500 O HOH A 521 O HOH A 645 0.38 REMARK 500 O HOH A 450 O HOH A 470 0.47 REMARK 500 O HOH A 452 O HOH A 479 0.60 REMARK 500 O HOH A 519 O HOH A 639 0.67 REMARK 500 O HOH A 517 O HOH A 600 0.73 REMARK 500 O HOH A 401 O HOH A 417 0.80 REMARK 500 O HOH A 539 O HOH A 647 0.84 REMARK 500 O HOH A 584 O HOH A 655 0.85 REMARK 500 O HOH A 522 O HOH A 652 0.91 REMARK 500 O HOH A 605 O HOH A 650 1.02 REMARK 500 O HOH A 403 O HOH A 419 1.07 REMARK 500 O HOH A 606 O HOH A 651 1.13 REMARK 500 O HOH A 517 O HOH A 640 1.17 REMARK 500 O HOH A 404 O HOH A 439 1.18 REMARK 500 O HOH A 475 O HOH A 496 1.19 REMARK 500 O HOH A 459 O HOH A 630 1.33 REMARK 500 O HOH A 601 O HOH A 653 1.35 REMARK 500 O HOH A 600 O HOH A 640 1.54 REMARK 500 O HOH A 437 O HOH A 536 1.56 REMARK 500 O HOH A 564 O HOH A 626 1.61 REMARK 500 O HOH A 524 O HOH A 620 1.65 REMARK 500 O HOH A 604 O HOH A 643 1.67 REMARK 500 O HOH A 586 O HOH A 649 1.72 REMARK 500 O HOH A 439 O HOH A 497 1.73 REMARK 500 O HOH A 547 O HOH A 653 1.80 REMARK 500 O HOH A 595 O HOH A 634 1.93 REMARK 500 O HOH A 437 O HOH A 489 2.00 REMARK 500 O HOH A 634 O HOH A 654 2.02 REMARK 500 O HOH A 476 O HOH A 591 2.03 REMARK 500 O HOH A 583 O HOH A 652 2.06 REMARK 500 NE2 GLN A 162 O LYS A 164 2.11 REMARK 500 O THR A 134 O HOH A 639 2.15 REMARK 500 O HOH A 644 O HOH A 654 2.15 REMARK 500 O HOH A 455 O HOH A 494 2.17 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 479 O HOH A 495 2555 0.04 REMARK 500 O HOH A 452 O HOH A 495 2555 0.59 REMARK 500 O HOH A 513 O HOH A 542 2454 1.09 REMARK 500 O HOH A 487 O HOH A 502 2444 1.34 REMARK 500 O HOH A 465 O HOH A 494 2545 1.70 REMARK 500 O HOH A 458 O HOH A 502 2444 2.06 REMARK 500 O HOH A 513 O HOH A 541 2454 2.14 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 GLU A 174 CG GLU A 174 CD -0.099 REMARK 500 GLU A 214 CB GLU A 214 CG -0.123 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 ASP A 132 CB - CG - OD2 ANGL. DEV. = 7.1 DEGREES REMARK 500 LEU A 133 CA - CB - CG ANGL. DEV. = 22.4 DEGREES REMARK 500 GLU A 174 OE1 - CD - OE2 ANGL. DEV. = 9.3 DEGREES REMARK 500 GLU A 214 CA - CB - CG ANGL. DEV. = 15.6 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 ALA A 161 -75.45 -110.19 REMARK 500 LEU A 168 -3.55 71.78 REMARK 500 ASP A 191 -74.32 -138.56 REMARK 500 CYS A 233 21.83 -142.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLN A 162 ASP A 163 124.61 REMARK 500 PHE A 263 ALA A 264 135.32 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 CU A 301 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 194 ND1 REMARK 620 2 CYS A 229 SG 120.1 REMARK 620 3 CYS A 233 SG 103.7 113.7 REMARK 620 4 MET A 240 SD 98.4 113.2 105.8 REMARK 620 5 CU A 302 CU 139.4 57.7 56.6 120.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 302 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 229 SG REMARK 620 2 GLU A 231 O 90.5 REMARK 620 3 CYS A 233 SG 116.5 105.0 REMARK 620 4 HIS A 237 ND1 121.2 93.6 118.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4TXV RELATED DB: PDB DBREF 4W9Z A 128 265 UNP H7C6E5 H7C6E5_BRADU 128 265 SEQADV 4W9Z MET A 127 UNP H7C6E5 INITIATING METHIONINE SEQRES 1 A 139 MET VAL PRO LYS ALA ASP LEU THR ILE LYS ALA THR GLY SEQRES 2 A 139 LYS GLN TRP TYR TRP SER TYR ALA TYR PRO ASP ASN GLY SEQRES 3 A 139 LYS PHE GLU PHE ASP SER LEU MET ALA GLN ASP LYS GLN SEQRES 4 A 139 PRO ARG LEU LEU GLY VAL ASP ASN GLU MET VAL VAL PRO SEQRES 5 A 139 VAL ASN LYS VAL ILE ARG VAL GLN VAL THR GLY ALA ASP SEQRES 6 A 139 VAL ILE HIS ALA PHE ALA LEU PRO ALA PHE GLY VAL LYS SEQRES 7 A 139 ILE ASP ALA ILE PRO GLY ARG LEU ASN GLU THR TRP PHE SEQRES 8 A 139 LYS ALA ALA LYS THR GLY MET PHE TYR GLY GLN CYS SER SEQRES 9 A 139 GLU LEU CYS GLY LYS ASP HIS ALA PHE MET PRO ILE ALA SEQRES 10 A 139 ILE ARG VAL VAL GLU ASP LYS GLU PHE ALA SER TRP VAL SEQRES 11 A 139 GLU THR ALA LYS LYS LYS PHE ALA SER HET CU A 301 1 HET CU A 302 1 HETNAM CU COPPER (II) ION FORMUL 2 CU 2(CU 2+) FORMUL 4 HOH *256(H2 O) HELIX 1 AA1 PRO A 199 GLY A 202 5 4 HELIX 2 AA2 ASP A 236 MET A 240 5 5 HELIX 3 AA3 GLU A 248 PHE A 263 1 16 SHEET 1 AA1 5 GLU A 155 SER A 158 0 SHEET 2 AA1 5 TYR A 143 ALA A 147 -1 N TRP A 144 O SER A 158 SHEET 3 AA1 5 LEU A 133 LYS A 140 -1 N THR A 138 O SER A 145 SHEET 4 AA1 5 VAL A 182 GLY A 189 1 O GLN A 186 N ALA A 137 SHEET 5 AA1 5 ASN A 213 LYS A 218 -1 O PHE A 217 N ILE A 183 SHEET 1 AA2 5 MET A 175 PRO A 178 0 SHEET 2 AA2 5 ILE A 242 VAL A 247 1 O ALA A 243 N MET A 175 SHEET 3 AA2 5 GLY A 223 CYS A 229 -1 N GLY A 223 O VAL A 246 SHEET 4 AA2 5 HIS A 194 LEU A 198 -1 N ALA A 197 O GLN A 228 SHEET 5 AA2 5 VAL A 203 ALA A 207 -1 O ALA A 207 N HIS A 194 LINK ND1 HIS A 194 CU CU A 301 1555 1555 2.03 LINK SG CYS A 229 CU CU A 301 1555 1555 2.34 LINK SG CYS A 229 CU CU A 302 1555 1555 2.32 LINK O GLU A 231 CU CU A 302 1555 1555 2.40 LINK SG CYS A 233 CU CU A 301 1555 1555 2.34 LINK SG CYS A 233 CU CU A 302 1555 1555 2.28 LINK ND1 HIS A 237 CU CU A 302 1555 1555 1.99 LINK SD MET A 240 CU CU A 301 1555 1555 2.44 LINK CU CU A 301 CU CU A 302 1555 1555 2.47 CISPEP 1 GLN A 141 TRP A 142 0 -0.61 CISPEP 2 GLN A 165 PRO A 166 0 -10.03 SITE 1 AC1 5 HIS A 194 CYS A 229 CYS A 233 MET A 240 SITE 2 AC1 5 CU A 302 SITE 1 AC2 5 CYS A 229 GLU A 231 CYS A 233 HIS A 237 SITE 2 AC2 5 CU A 301 CRYST1 32.431 38.612 59.644 90.00 97.63 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 0.030835 0.000000 0.004133 0.00000 SCALE2 0.000000 0.025899 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016916 0.00000